From 625193a82a4a404c7c069f479c704172b2f74f16 Mon Sep 17 00:00:00 2001 From: Thierry Gosselin Date: Wed, 6 Nov 2024 11:43:20 -0500 Subject: [PATCH] # radiator 1.3.5 2024-11-06 * Fix the one column matrices in dplyr::filter warning. * Fix the error when dplyr::select couldn't find the column STRATA. --- .DS_Store | Bin 6148 -> 6148 bytes DESCRIPTION | 6 +- NEWS.md | 7 ++ R/filter_genotyping.R | 4 +- R/filter_ma.R | 5 +- R/filter_rad.R | 4 +- R/radiator_tidy.R | 3 +- README.md | 4 +- docs/404.html | 16 ++--- docs/LICENSE.html | 16 ++--- docs/articles/get_started.html | 23 +++---- docs/articles/index.html | 16 ++--- docs/articles/life_cycle.html | 19 +++--- .../articles/rad_genomics_computer_setup.html | 51 +++++++------- docs/authors.html | 24 +++---- docs/index.html | 20 +++--- docs/news/index.html | 21 +++--- docs/pkgdown.yml | 7 +- docs/reference/Exposition_pipe_operator.html | 16 ++--- docs/reference/allele_count.html | 16 ++--- docs/reference/allele_frequencies.html | 28 ++++---- docs/reference/assign_defaults.html | 16 ++--- docs/reference/bayescan_one.html | 16 ++--- docs/reference/betas_estimator.html | 34 +++++----- docs/reference/blacklist_hw.html | 16 ++--- docs/reference/boxplot_stats.html | 16 ++--- docs/reference/calibrate_alleles.html | 32 ++++----- docs/reference/change_pop_names.html | 24 ++++--- docs/reference/check_args_class.html | 16 ++--- docs/reference/check_dart.html | 16 ++--- docs/reference/check_header_source_vcf.html | 16 ++--- docs/reference/check_pop_levels.html | 24 ++++--- docs/reference/clean_dart_colnames.html | 16 ++--- docs/reference/clean_dart_locus.html | 16 ++--- docs/reference/clean_ind_names.html | 20 +++--- docs/reference/clean_markers_names.html | 20 +++--- docs/reference/clean_pop_names.html | 20 +++--- .../compound_assignment_pipe_operator.html | 16 ++--- docs/reference/compute_maf.html | 16 ++--- docs/reference/count_monomorphic.html | 16 ++--- docs/reference/dart2gds.html | 16 ++--- docs/reference/data_info.html | 16 ++--- docs/reference/detect_all_missing.html | 24 +++---- docs/reference/detect_allele_problems.html | 40 +++++------ docs/reference/detect_biallelic_markers.html | 28 ++++---- docs/reference/detect_biallelic_problems.html | 28 ++++---- docs/reference/detect_dart_format.html | 16 ++--- docs/reference/detect_duplicate_genomes.html | 48 ++++++------- docs/reference/detect_genomic_format.html | 28 ++++---- docs/reference/detect_het_outliers.html | 42 ++++++------ docs/reference/detect_microsatellites.html | 32 ++++----- docs/reference/detect_mixed_genomes.html | 44 ++++++------ docs/reference/detect_paralogs.html | 38 +++++------ docs/reference/detect_ref_genome.html | 32 ++++----- docs/reference/diagnostic_maf.html | 28 ++++---- docs/reference/distance2tibble.html | 16 ++--- docs/reference/distance_individuals.html | 16 ++--- docs/reference/erase_genotypes.html | 34 +++++----- docs/reference/estimate_m.html | 30 ++++---- docs/reference/extract_coverage.html | 42 ++++++------ docs/reference/extract_dart_target_id.html | 38 +++++------ docs/reference/extract_data_source.html | 16 ++--- docs/reference/extract_dots.html | 16 ++--- .../reference/extract_genotypes_metadata.html | 36 +++++----- .../extract_individuals_metadata.html | 30 ++++---- docs/reference/extract_individuals_vcf.html | 28 ++++---- docs/reference/extract_info_vcf.html | 16 ++--- docs/reference/extract_markers_metadata.html | 30 ++++---- .../reference/filter_blacklist_genotypes.html | 32 +++++---- docs/reference/filter_common_markers.html | 38 +++++------ docs/reference/filter_coverage.html | 44 ++++++------ .../filter_dart_reproducibility.html | 38 +++++------ docs/reference/filter_fis.html | 34 +++++----- docs/reference/filter_genotyping.html | 44 ++++++------ docs/reference/filter_het.html | 50 +++++++------- docs/reference/filter_hwe.html | 46 ++++++------- docs/reference/filter_individuals.html | 46 ++++++------- docs/reference/filter_ld.html | 42 ++++++------ docs/reference/filter_monomorphic.html | 36 +++++----- docs/reference/filter_rad.html | 46 ++++++------- docs/reference/filter_snp_number.html | 42 ++++++------ docs/reference/filter_snp_position_read.html | 42 ++++++------ docs/reference/filter_whitelist.html | 30 ++++---- docs/reference/folder_prefix.html | 16 ++--- docs/reference/folder_short.html | 20 +++--- docs/reference/gds2tidy.html | 16 ++--- docs/reference/generate_filename.html | 16 ++--- docs/reference/generate_folder.html | 32 +++++---- .../generate_geno_freq_boundaries.html | 16 ++--- docs/reference/generate_hzar.html | 16 ++--- docs/reference/generate_markers_metadata.html | 38 +++++------ .../reference/generate_squeleton_folders.html | 16 ++--- docs/reference/generate_strata.html | 22 +++--- docs/reference/generate_whitelist.html | 16 ++--- docs/reference/genome_similarity.html | 16 ++--- docs/reference/genomic_converter.html | 50 +++++++------- docs/reference/gt2array.html | 16 ++--- docs/reference/haplotype_reconstruction.html | 22 +++--- docs/reference/hwe_analysis.html | 16 ++--- docs/reference/ibdg_fh.html | 44 ++++++------ docs/reference/import_dart.html | 16 ++--- docs/reference/ind_total_reads.html | 16 ++--- docs/reference/index.html | 18 ++--- docs/reference/individuals2strata.html | 34 +++++----- docs/reference/join_strata.html | 34 +++++----- docs/reference/ld2df.html | 16 ++--- docs/reference/ld_boxplot.html | 16 ++--- docs/reference/ld_missing.html | 40 +++++------ docs/reference/ld_pruning.html | 30 ++++---- docs/reference/list_filters.html | 24 ++++--- docs/reference/markers_genotyped_helper.html | 16 ++--- docs/reference/merge_dart.html | 46 ++++++------- docs/reference/message_func_call.html | 16 ++--- docs/reference/missing_per_pop.html | 16 ++--- docs/reference/n.html | 16 ++--- docs/reference/not_common_markers.html | 16 ++--- docs/reference/parallel_core_opt.html | 16 ++--- docs/reference/parse_gds_metadata.html | 16 ++--- docs/reference/pi.html | 36 +++++----- docs/reference/pi_pop.html | 16 ++--- docs/reference/pi_rad.html | 16 ++--- docs/reference/pipe.html | 16 ++--- docs/reference/plot_bayescan.html | 16 ++--- docs/reference/plot_boxplot_coverage.html | 20 +++--- docs/reference/plot_boxplot_diversity.html | 34 +++++----- .../plot_coverage_imbalance_diagnostic.html | 32 ++++----- .../plot_density_distribution_coverage.html | 24 ++++--- .../plot_density_distribution_het.html | 30 ++++---- .../plot_density_distribution_maf.html | 28 ++++---- .../plot_distribution_diversity.html | 28 ++++---- docs/reference/plot_het_outliers.html | 16 ++--- docs/reference/plot_snp_number_loci.html | 22 +++--- docs/reference/plot_snp_position_read.html | 24 ++++--- docs/reference/plot_upset.html | 16 ++--- docs/reference/private_alleles.html | 32 ++++----- docs/reference/private_haplotypes.html | 28 ++++---- docs/reference/radiator_common_arguments.html | 32 +++++---- docs/reference/radiator_dots.html | 32 +++++---- docs/reference/radiator_folder.html | 24 ++++--- docs/reference/radiator_function_header.html | 16 ++--- docs/reference/radiator_gds.html | 16 ++--- docs/reference/radiator_gds_skeleton.html | 16 ++--- docs/reference/radiator_packages_dep.html | 16 ++--- docs/reference/radiator_parameters.html | 16 ++--- docs/reference/radiator_pkg_install.html | 22 +++--- docs/reference/radiator_question.html | 16 ++--- docs/reference/radiator_results_message.html | 16 ++--- docs/reference/radiator_snakecase.html | 16 ++--- docs/reference/radiator_split_tibble.html | 16 ++--- docs/reference/radiator_tic.html | 16 ++--- docs/reference/radiator_toc.html | 16 ++--- docs/reference/read_blacklist_genotypes.html | 30 ++++---- docs/reference/read_blacklist_id.html | 30 ++++---- docs/reference/read_dart.html | 46 ++++++------- docs/reference/read_plink.html | 38 +++++------ docs/reference/read_rad.html | 44 ++++++------ docs/reference/read_strata.html | 50 +++++++------- docs/reference/read_vcf.html | 46 ++++++------- docs/reference/read_whitelist.html | 26 +++---- docs/reference/remove_duplicates.html | 30 ++++---- docs/reference/replace_by_na.html | 16 ++--- docs/reference/reset_filters.html | 62 +++++++++-------- docs/reference/run_bayescan.html | 62 +++++++---------- docs/reference/separate_gt.html | 16 ++--- docs/reference/separate_markers.html | 44 ++++++------ docs/reference/sex_markers_plot.html | 16 ++--- docs/reference/sexy_markers.html | 56 +++++++-------- .../simulate_genos_from_posterior.html | 24 ++++--- docs/reference/split_tibble_rows.html | 16 ++--- docs/reference/split_vcf.html | 34 +++++----- docs/reference/strata_haplo.html | 16 ++--- docs/reference/subsampling_data.html | 16 ++--- docs/reference/summarise_genotypes.html | 16 ++--- docs/reference/summarize_sex.html | 16 ++--- docs/reference/summary_gds.html | 24 ++++--- docs/reference/summary_rad.html | 26 +++---- docs/reference/summary_strata.html | 25 +++---- docs/reference/switch_allele_count.html | 16 ++--- docs/reference/switch_genotypes.html | 16 ++--- docs/reference/sync_gds.html | 32 +++++---- docs/reference/tibble_stats.html | 16 ++--- docs/reference/tidy2gds.html | 16 ++--- docs/reference/tidy2wide.html | 16 ++--- docs/reference/tidy_dart_metadata.html | 34 +++++----- docs/reference/tidy_fstat.html | 34 +++++----- docs/reference/tidy_genepop.html | 34 +++++----- docs/reference/tidy_genind.html | 28 ++++---- docs/reference/tidy_genlight.html | 30 ++++---- docs/reference/tidy_genomic_data.html | 42 ++++++------ docs/reference/tidy_gtypes.html | 20 +++--- docs/reference/tidy_plink.html | 38 +++++------ docs/reference/tidy_vcf.html | 42 ++++++------ docs/reference/tidy_wide.html | 26 +++---- docs/reference/update_bl_individuals.html | 16 ++--- docs/reference/update_bl_markers.html | 16 ++--- docs/reference/update_filter_parameter.html | 16 ++--- docs/reference/update_radiator_gds.html | 16 ++--- docs/reference/vcf_strata.html | 28 ++++---- docs/reference/write_arlequin.html | 30 ++++---- docs/reference/write_bayescan.html | 32 ++++----- docs/reference/write_betadiv.html | 24 +++---- docs/reference/write_colony.html | 64 +++++++++--------- docs/reference/write_dadi.html | 40 +++++------ docs/reference/write_fasta.html | 16 ++--- docs/reference/write_faststructure.html | 32 ++++----- docs/reference/write_fineradstructure.html | 30 ++++---- docs/reference/write_gds.html | 38 +++++------ docs/reference/write_genepop.html | 34 +++++----- docs/reference/write_genepopedit.html | 24 +++---- docs/reference/write_genind.html | 24 ++++--- docs/reference/write_genlight.html | 34 +++++----- docs/reference/write_gsi_sim.html | 32 ++++----- docs/reference/write_gtypes.html | 32 ++++----- docs/reference/write_hapmap.html | 22 +++--- docs/reference/write_hierfstat.html | 26 +++---- docs/reference/write_hzar.html | 34 +++++----- docs/reference/write_ldna.html | 26 +++---- docs/reference/write_maverick.html | 28 ++++---- docs/reference/write_pcadapt.html | 34 +++++----- docs/reference/write_plink.html | 22 +++--- docs/reference/write_rad.html | 44 ++++++------ docs/reference/write_related.html | 30 ++++---- docs/reference/write_rubias.html | 30 ++++---- docs/reference/write_snprelate.html | 34 +++++----- docs/reference/write_stockr.html | 28 ++++---- docs/reference/write_structure.html | 30 ++++---- docs/reference/write_vcf.html | 28 ++++---- vignettes/rad_genomics_computer_setup.Rmd | 27 ++++---- vignettes/rad_genomics_computer_setup.html | 36 +++++----- 229 files changed, 2994 insertions(+), 2928 deletions(-) diff --git a/.DS_Store b/.DS_Store index 7727bf7ffdd18e8ecbcb4b2416aa67351886c8d2..ea67c66406be4efeb9246e36c4cd04d20831f4b9 100644 GIT binary patch delta 31 ncmZoMXfc@J&nU4mU^g?P#AF_p`= threshold)) + if (rlang::has_name(x, stats)) nrow(dplyr::filter(.data = x, x[[stats]] >= threshold)) }#End how_many_markers end.seq <- ceiling(0.2 * n.diplo.samples) @@ -453,7 +453,8 @@ filter_ma <- function( ) %>% readr::write_tsv( x = ., - file = file.path(path.folder, "mac.helper.table.tsv")) + file = file.path(path.folder, "mac.helper.table.tsv") + ) # if (verbose) message("File written: mac.helper.table.tsv") diff --git a/R/filter_rad.R b/R/filter_rad.R index 6d4aa910..ed94d319 100644 --- a/R/filter_rad.R +++ b/R/filter_rad.R @@ -786,7 +786,7 @@ filter_rad <- function( filter.long.ld = filter.long.ld.bk, parallel.core = parallel.core, filename = NULL, - iiiiverbose = verbose, + verbose = verbose, long.ld.missing = long.ld.missing.bk, ld.method = ld.method.bk, parameters = filters.parameters, @@ -895,7 +895,7 @@ filter_rad <- function( path = path.folder, filename = "strata.filtered.tsv", tsv = TRUE, - write.message = "Writing the filtered strata: strata.filtered.tsv", + write.message = "Writing the filtered strata: ", verbose = verbose) diff --git a/R/radiator_tidy.R b/R/radiator_tidy.R index cd13e814..fbe29a10 100644 --- a/R/radiator_tidy.R +++ b/R/radiator_tidy.R @@ -426,7 +426,8 @@ tidy_genomic_data <- function( # Strata---------------------------------------------------------------------- strata.df <- read_strata( strata = strata, - pop.id = TRUE, + pop.id = FALSE, + # pop.id = TRUE, blacklist.id = blacklist.id, verbose = verbose) %$% strata diff --git a/README.md b/README.md index 10fd3403..a5844eb4 100644 --- a/README.md +++ b/README.md @@ -5,8 +5,8 @@ [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) -[![packageversion](https://img.shields.io/badge/Package%20version-1.3.4-orange.svg)](commits/master) -[![Last-changedate](https://img.shields.io/badge/last%20change-2024--06--05-brightgreen.svg)](/commits/master) +[![packageversion](https://img.shields.io/badge/Package%20version-1.3.5-orange.svg)](commits/master) +[![Last-changedate](https://img.shields.io/badge/last%20change-2024--11--06-brightgreen.svg)](/commits/master) [![R-CMD-check](https://github.com/thierrygosselin/radiator/workflows/R-CMD-check/badge.svg)](https://github.com/thierrygosselin/radiator/actions) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3687060.svg)](https://doi.org/10.5281/zenodo.3687060) diff --git a/docs/404.html b/docs/404.html index 3620659c..deafe35a 100644 --- a/docs/404.html +++ b/docs/404.html @@ -18,7 +18,7 @@ - +
@@ -50,7 +50,7 @@
  • @@ -81,7 +81,7 @@
    • - +
    @@ -109,16 +109,16 @@

    Page not found (404)

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 59373bf2..c958d3ec 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -277,15 +277,15 @@

    How to Apply These Terms

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/get_started.html b/docs/articles/get_started.html index ecb6bdac..e9448a8e 100644 --- a/docs/articles/get_started.html +++ b/docs/articles/get_started.html @@ -12,14 +12,13 @@ - - +
    @@ -51,7 +50,7 @@
  • @@ -82,7 +81,7 @@
    • - +
    @@ -91,7 +90,7 @@

    Get Started

    Thierry Gosselin

    -

    2024-06-05

    +

    2024-11-06

    Source: vignettes/get_started.Rmd @@ -289,9 +288,7 @@

    Overview - -

    +
    @@ -304,16 +301,16 @@

    Overview

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/index.html b/docs/articles/index.html index a271d546..3ddf55e9 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -85,15 +85,15 @@

    All vignettes

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/life_cycle.html b/docs/articles/life_cycle.html index 27bd6f88..4087aec9 100644 --- a/docs/articles/life_cycle.html +++ b/docs/articles/life_cycle.html @@ -12,14 +12,13 @@ - - +
    @@ -51,7 +50,7 @@
  • @@ -82,7 +81,7 @@
    • - +
    @@ -91,7 +90,7 @@

    Life Cycle

    Thierry Gosselin

    -

    2024-06-05

    +

    2024-11-06

    Source: vignettes/life_cycle.Rmd @@ -148,16 +147,16 @@

    2024-06-05

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/rad_genomics_computer_setup.html b/docs/articles/rad_genomics_computer_setup.html index 60ddacb2..e72b114b 100644 --- a/docs/articles/rad_genomics_computer_setup.html +++ b/docs/articles/rad_genomics_computer_setup.html @@ -12,14 +12,13 @@ - - +
    @@ -51,7 +50,7 @@
  • @@ -82,7 +81,7 @@
    • - +
    @@ -90,7 +89,7 @@

    RADseq Genomics in R

    computer setup

    -

    2024-06-05

    +

    2024-11-06

    Source: vignettes/rad_genomics_computer_setup.Rmd @@ -139,7 +138,7 @@

    macOS

    Update your OS

      -
    • the current version is macOS Ventura 13.0
      • +
    • the current version is macOS Sequoia 15.1
    • how to update
    @@ -210,24 +209,24 @@

    Update GCClink.

    -

    Ventura and Monterey gcc-11.2-bin.tar.gz

    +

    Sonoma gcc-14.1-m1-bin.tar.gz

    #In Terminal
 cd Downloads
-sudo tar -zxvf gcc-11.2-bin.tar.gz -C /usr/local --strip-components=2
    -
    sudo rm gcc-11.2-bin.tar.gz
+sudo tar -zxvf gcc-14.1-m1-bin.tar.gz -C /usr/local --strip-components=2
    +
    sudo rm gcc-14.1-m1-bin.tar.gz
 gcc -v

    Update Clang

    We want clang -compiler with OpenMP enabled. The latest version is 15.0.3.

    -
    #In browser
-https://github.com/llvm/llvm-project/releases/download/llvmorg-15.0.3/clang+llvm-15.0.3-x86_64-apple-darwin.tar.xz
+compiler with OpenMP enabled. The latest version is 19.1.3.
    
+
    #In browser make sure you know if your mac as an Intel or Mac chips (M1, M2, etc)
+https://github.com/llvm/llvm-project/releases/download/llvmorg-19.1.3/LLVM-19.1.3-macOS-X64.tar.xz
 #In Terminal
 cd Downloads
-sudo tar -xzvf clang+llvm-15.0.3-x86_64-apple-darwin.tar.xz -C/usr/local --strip-components=1
    
-
    sudo rm clang+llvm-15.0.3-x86_64-apple-darwin.tar.xz
+sudo tar -xzvf LLVM-19.1.3-macOS-X64.tar.xz -C/usr/local --strip-components=1
    
+
    sudo rm LLVM-19.1.3-macOS-X64.tar.xz
 clang -v
    @@ -304,11 +303,11 @@

    Linux

    Install R

    -

    To install R v4.2.1 “Funny-Looking Kid” released on -2022-06-23 download the installer and follow the instructions

    +

    To install R v4.4.2 “Pile of Leaves” released on +2024-10-31 download the installer and follow the instructions

    # for macOS
 cd Downloads
-curl -O https://cran.r-project.org/bin/macosx/R-4.2.1.pkg
    +curl -O https://cran.r-project.org/bin/macosx/R-4.4.2.pkg

    To remove R completely from macOS

    sudo rm -rf /Library/Frameworks/R.framework /Applications/R.app \
 /usr/bin/R /usr/bin/Rscript
    @@ -726,14 +725,14 @@

    Better to install and compile them from source to enable OpenMP. Install in the terminal zstd and lz4:

    cd ~/Downloads
-curl -L https://github.com/lz4/lz4/archive/refs/tags/v1.9.4.tar.gz | tar xf -
+curl -L https://github.com/lz4/lz4/archive/refs/tags/v1.10.0.tar.gz | tar xf -
 cd lz4*
 make 
 sudo make install
 cd .. 
 sudo rm -R lz4*
    cd ~/Downloads
-curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.5.tar.gz | tar xf -
+curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.6.tar.gz | tar xf -
 cd zstd*
 make 
 sudo make install
@@ -1157,9 +1156,7 @@ 
    Shortcut to folder path
 
-        
-
    +

    @@ -1172,16 +1169,16 @@

    Shortcut to folder path

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/authors.html b/docs/authors.html index b256eb29..fbe32a19 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -66,17 +66,17 @@

    Authors and Citation

    - +
    • -

      Thierry Gosselin. Author, maintainer. +

      Thierry Gosselin. Author, maintainer.

    • -

      Manuel Lamothe. Contributor. +

      Manuel Lamothe. Contributor.

    • -

      Floriaan Devloo-Delva. Contributor. +

      Floriaan Devloo-Delva. Contributor.

    @@ -108,15 +108,15 @@

    Citation

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/index.html b/docs/index.html index 6fa0528e..68305c28 100644 --- a/docs/index.html +++ b/docs/index.html @@ -19,7 +19,7 @@ - +
    @@ -51,7 +51,7 @@
  • @@ -82,7 +82,7 @@
    • - +
    @@ -177,8 +177,8 @@

    Dev status

    • lifecycle
    • Project Status: Active – The project has reached a stable, usable state and is being actively developed.
      • -
    • packageversion
      • -
    • Last-changedate
      • +
    • packageversion
      • +
    • Last-changedate
    • R-CMD-check
    • DOI
    @@ -195,16 +195,16 @@

    Dev status

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/news/index.html b/docs/news/index.html index 781ef5fc..7cd4e627 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -66,6 +66,11 @@

    Changelog

    Source: NEWS.md
    +
    +

    radiator 1.3.5 2024-11-06

    +
    • Fix the one column matrices in dplyr::filter warning.
      • +
    • Fix the error when dplyr::select couldn’t find the column STRATA.
      • +

    radiator 1.3.4 2024-06-05

    • Open the parallel.core argument for some internal functions to help windows users with parallel processing problems in R. #188
      • @@ -354,15 +359,15 @@

      radia

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 3a63b8e8..88480833 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,9 +1,8 @@ -pandoc: 3.1.11 -pkgdown: 2.0.9 +pandoc: '3.2' +pkgdown: 2.1.1 pkgdown_sha: ~ articles: get_started: get_started.html life_cycle: life_cycle.html rad_genomics_computer_setup: rad_genomics_computer_setup.html -last_built: 2024-06-05T15:36Z - +last_built: 2024-11-06T16:41Z diff --git a/docs/reference/Exposition_pipe_operator.html b/docs/reference/Exposition_pipe_operator.html index bc788b31..cfff308c 100644 --- a/docs/reference/Exposition_pipe_operator.html +++ b/docs/reference/Exposition_pipe_operator.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    Exposition pipe-operator

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/allele_count.html b/docs/reference/allele_count.html index f34a0bbf..b42b6e8a 100644 --- a/docs/reference/allele_count.html +++ b/docs/reference/allele_count.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    allele_count

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/allele_frequencies.html b/docs/reference/allele_frequencies.html index 3ef7bd15..a90ce061 100644 --- a/docs/reference/allele_frequencies.html +++ b/docs/reference/allele_frequencies.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -85,20 +85,22 @@

    Compute allele frequencies per markers and populations

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    verbose
    +
    verbose

    (optional, logical) verbose = TRUE to be chatty during execution. Default: verbose = TRUE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    @@ -106,9 +108,7 @@

    Arguments

    Value

    - - -

    A list with allele frequencies in a data frame in long and wide format, +

    A list with allele frequencies in a data frame in long and wide format, and a matrix. Local (pop) and global minor allele frequency (MAF) is also computed.

    @@ -128,15 +128,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/assign_defaults.html b/docs/reference/assign_defaults.html index 040659d9..73b9542d 100644 --- a/docs/reference/assign_defaults.html +++ b/docs/reference/assign_defaults.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    assign_defaults

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/bayescan_one.html b/docs/reference/bayescan_one.html index 61dfbf1f..c4104aec 100644 --- a/docs/reference/bayescan_one.html +++ b/docs/reference/bayescan_one.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -103,15 +103,15 @@

    bayescan one iteration

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/betas_estimator.html b/docs/reference/betas_estimator.html index 74a8698d..b2599c8f 100644 --- a/docs/reference/betas_estimator.html +++ b/docs/reference/betas_estimator.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,7 +77,9 @@

    Estimate \(\beta\)s per population

    Arguments

    -
    data
    + + +
    data

    14 options for input (diploid data only): VCFs (SNPs or Haplotypes, to make the vcf population ready), plink (tped, bed), stacks haplotype file, genind (library(adegenet)), @@ -93,7 +95,7 @@

    Arguments

    to understand it's limit before asking raditor to convert or filter your dataset.

    -
    strata
    +
    strata

    (optional) The strata file is a tab delimited file with a minimum of 2 columns headers: INDIVIDUALS and STRATA. Documented in read_strata. @@ -103,7 +105,7 @@

    Arguments

    Default: strata = NULL.

    -
    filename
    +
    filename

    (optional) The function uses write.fst, to write the tidy data frame in the working directory. The file extension appended to @@ -112,7 +114,7 @@

    Arguments

    in the global environment only (i.e. not written in the working directory...).

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -120,9 +122,7 @@

    Arguments

    Value

    - - -

    A list is created with 3 objects: +

    A list is created with 3 objects: betaiovl: Average \(\beta_i\) over loci, Hw: Within population gene diversities Hb: Between populations gene diversities

    @@ -145,7 +145,7 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # Using a  VCF file, the simplest for of the function:
 fh <- ibdg_fh(
 data = "batch_1.vcf",
@@ -157,7 +157,7 @@ 
    Examples
    
 fh$fh.manhattan.plot
 # To view the distribution of FH values:
 fh$fh.distribution.plot
-}
+} # }
    @@ -172,15 +172,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/blacklist_hw.html b/docs/reference/blacklist_hw.html index 93cee9bb..ac363282 100644 --- a/docs/reference/blacklist_hw.html +++ b/docs/reference/blacklist_hw.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -99,15 +99,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/boxplot_stats.html b/docs/reference/boxplot_stats.html index 31aad607..82677f11 100644 --- a/docs/reference/boxplot_stats.html +++ b/docs/reference/boxplot_stats.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -101,15 +101,15 @@

    boxplot_stats

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/calibrate_alleles.html b/docs/reference/calibrate_alleles.html index 1a4455e7..53905e4d 100644 --- a/docs/reference/calibrate_alleles.html +++ b/docs/reference/calibrate_alleles.html @@ -10,7 +10,7 @@ - +
    @@ -41,7 +41,7 @@
    • - +
    @@ -97,40 +97,40 @@

    Calibrate REF and ALT alleles based on count

    Arguments

    -
    data
    + + +
    data

    A genomic data set in the global environment tidy formats. See details for more info.

    -
    biallelic
    +
    biallelic

    (optional) If biallelic = TRUE/FALSE will be use during multiallelic REF/ALT decision and speed up computations. Default: biallelic = NULL.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution. This is no longer used. The code is as fast as it can. Using more cores will reduce the speed. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) verbose = TRUE to be chatty during execution. Default: verbose = FALSE.

    -
    ...
    +
    ...

    (optional) To pass further argument for fine-tuning the tidying (details below).

    Value

    - - -

    Depending if the input file is biallelic or multiallelic, +

    Depending if the input file is biallelic or multiallelic, the function will output additional to REF and ALT column several genotype codings:

    • GT: the genotype in 6 digits format with integers.

    • GT_VCF: the genotype in VCF format with integers.

    • GT_VCF_NUC: the genotype in VCF format with letters corresponding to nucleotide.

      • @@ -165,15 +165,15 @@

      Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/change_pop_names.html b/docs/reference/change_pop_names.html index b690e7e8..7fbf3d60 100644 --- a/docs/reference/change_pop_names.html +++ b/docs/reference/change_pop_names.html @@ -4,7 +4,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -79,7 +79,9 @@

    Transform into a factor the STRATA column, change names and reorder the leve

    Arguments

    -
    data
    + + +
    data

    14 options for input (diploid data only): VCFs (SNPs or Haplotypes, to make the vcf population ready), plink (tped, bed), stacks haplotype file, genind (library(adegenet)), @@ -95,7 +97,7 @@

    Arguments

    to understand it's limit before asking raditor to convert or filter your dataset.

    -
    pop.levels
    +
    pop.levels

    (optional, string) This refers to the levels in a factor. In this case, the id of the pop. Use this argument to have the pop ordered your way instead of the default @@ -105,7 +107,7 @@

    Arguments

    Default: pop.levels = NULL.

    -
    pop.labels
    +
    pop.labels

    (optional, string) Use this argument to rename/relabel your pop or combine your pop. e.g. To combine "QUE" and "ONT" into a new pop called "NEW": @@ -144,15 +146,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/check_args_class.html b/docs/reference/check_args_class.html index c51c69c9..2126a452 100644 --- a/docs/reference/check_args_class.html +++ b/docs/reference/check_args_class.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    check_args_class

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/check_dart.html b/docs/reference/check_dart.html index b84e8644..18e4c2b2 100644 --- a/docs/reference/check_dart.html +++ b/docs/reference/check_dart.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    check_dart

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/check_header_source_vcf.html b/docs/reference/check_header_source_vcf.html index 4f8954f4..2ce4148e 100644 --- a/docs/reference/check_header_source_vcf.html +++ b/docs/reference/check_header_source_vcf.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    Check the vcf header and detect vcf source

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/check_pop_levels.html b/docs/reference/check_pop_levels.html index bc4c7c45..c10d9501 100644 --- a/docs/reference/check_pop_levels.html +++ b/docs/reference/check_pop_levels.html @@ -4,7 +4,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -79,7 +79,9 @@

    Check the use of pop.levels, pop.labels and pop.select arguments.

    Arguments

    -
    pop.levels
    + + +
    pop.levels

    (optional, string) This refers to the levels in a factor. In this case, the id of the pop. Use this argument to have the pop ordered your way instead of the default @@ -89,7 +91,7 @@

    Arguments

    Default: pop.levels = NULL.

    -
    pop.labels
    +
    pop.labels

    (optional, string) Use this argument to rename/relabel your pop or combine your pop. e.g. To combine "QUE" and "ONT" into a new pop called "NEW": @@ -105,7 +107,7 @@

    Arguments

    White spaces in population names are replaced by underscore.

    -
    pop.select
    +
    pop.select

    (optional, string) Selected list of populations for the analysis. e.g. pop.select = c("QUE", "ONT") to select QUE and ONT population samples (out of 20 pops). @@ -129,15 +131,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/clean_dart_colnames.html b/docs/reference/clean_dart_colnames.html index b3153cf4..6a3a4eaf 100644 --- a/docs/reference/clean_dart_colnames.html +++ b/docs/reference/clean_dart_colnames.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -93,15 +93,15 @@

    clean_dart_colnames

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/clean_dart_locus.html b/docs/reference/clean_dart_locus.html index 5501a63e..d2fd01ed 100644 --- a/docs/reference/clean_dart_locus.html +++ b/docs/reference/clean_dart_locus.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    clean_dart_locus

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/clean_ind_names.html b/docs/reference/clean_ind_names.html index 72026c05..f1fa8470 100644 --- a/docs/reference/clean_ind_names.html +++ b/docs/reference/clean_ind_names.html @@ -8,7 +8,7 @@ - +
    @@ -39,7 +39,7 @@
    • - +
    @@ -87,7 +87,9 @@

    Clean individual's names for radiator and other packages

    Arguments

    -
    x
    + + +
    x

    (character string) Individuals character string.

    @@ -104,15 +106,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/clean_markers_names.html b/docs/reference/clean_markers_names.html index aef61a15..4dff32da 100644 --- a/docs/reference/clean_markers_names.html +++ b/docs/reference/clean_markers_names.html @@ -9,7 +9,7 @@ - +
    @@ -40,7 +40,7 @@
    • - +
    @@ -89,7 +89,9 @@

    Clean marker's names for radiator and other packages

    Arguments

    -
    x
    + + +
    x

    (character string) Markers character string.

    @@ -106,15 +108,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/clean_pop_names.html b/docs/reference/clean_pop_names.html index 97119315..035d1d1a 100644 --- a/docs/reference/clean_pop_names.html +++ b/docs/reference/clean_pop_names.html @@ -7,7 +7,7 @@ - +
    @@ -38,7 +38,7 @@
    • - +
    @@ -85,7 +85,9 @@

    Clean population's names for radiator and other packages

    Arguments

    -
    x
    + + +
    x

    (character string) Population character string.

    @@ -102,15 +104,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/compound_assignment_pipe_operator.html b/docs/reference/compound_assignment_pipe_operator.html index 1769835e..5c7a47e6 100644 --- a/docs/reference/compound_assignment_pipe_operator.html +++ b/docs/reference/compound_assignment_pipe_operator.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    compound assignment pipe operator

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/compute_maf.html b/docs/reference/compute_maf.html index 7e57f537..404a8792 100644 --- a/docs/reference/compute_maf.html +++ b/docs/reference/compute_maf.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    compute_maf

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/count_monomorphic.html b/docs/reference/count_monomorphic.html index 5b655ca5..8142b98b 100644 --- a/docs/reference/count_monomorphic.html +++ b/docs/reference/count_monomorphic.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    count_monomorphic

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/dart2gds.html b/docs/reference/dart2gds.html index cefb65dd..0d6ce83a 100644 --- a/docs/reference/dart2gds.html +++ b/docs/reference/dart2gds.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -99,15 +99,15 @@

    dart2gds

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/data_info.html b/docs/reference/data_info.html index 0d740e53..e02b2cb5 100644 --- a/docs/reference/data_info.html +++ b/docs/reference/data_info.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    data_info

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/detect_all_missing.html b/docs/reference/detect_all_missing.html index 0f65a14b..70af9352 100644 --- a/docs/reference/detect_all_missing.html +++ b/docs/reference/detect_all_missing.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -81,15 +81,15 @@

    Detect markers with all missing genotypes

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment.

    Value

    - - -

    The filtered dataset if problematic markers were found. Otherwise, +

    The filtered dataset if problematic markers were found. Otherwise, the untouch dataset.

    @@ -109,15 +109,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/detect_allele_problems.html b/docs/reference/detect_allele_problems.html index 8cdcbd02..eaa669af 100644 --- a/docs/reference/detect_allele_problems.html +++ b/docs/reference/detect_allele_problems.html @@ -11,7 +11,7 @@ - +
    @@ -42,7 +42,7 @@
    • - +
    @@ -93,14 +93,16 @@

    Detect alternate allele problems

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    allele.threshold
    +
    allele.threshold

    (integer) Threshold of alternate allele copies. Below this threshold markers are blacklisted. Choose this threshold based on your tolerance for uninformative or unreliable information and @@ -108,36 +110,28 @@

    Arguments

    See details for more info.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function (see details).

    Value

    - - -

    A list with summary, plot and blacklist. +

    A list with summary, plot and blacklist. Summary statistics for the blacklisted markers are generated and include coverage and genotype likelihood information.

    - -

    $alt.allele.count.plot: Distribution of marker's alternate allele number. The shape is usually skewed right.

    - -

    $alt.depth.count.distribution.plot: Distribution of markers alternate allele depth (in number of read). The range showed on the plot is between 1 and 10, and you decide your tolerance for low coverage and good genotype calls.

    - -

    This plot is associated with $number.markers, a table that shows the number of markers <= allele.threshold . Also in the table, the range of alternate allele read depth (1 to 10), same as plot but showing here @@ -181,7 +175,7 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 problem <- detect_allele_problems(
         data = salamander,
         strata = "strata.salmon.tsv",
@@ -190,7 +184,7 @@ 
    Examples
    
 # The default with this function:
 # filter.monomorphic = TRUE # = discarded
 # filter.common.markers = TRUE # markers not in common between pop are discarded
-}
+} # }
    @@ -205,15 +199,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/detect_biallelic_markers.html b/docs/reference/detect_biallelic_markers.html index b74a6d64..21e0efaa 100644 --- a/docs/reference/detect_biallelic_markers.html +++ b/docs/reference/detect_biallelic_markers.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -85,7 +85,9 @@

    Detect biallelic data

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -94,13 +96,13 @@

    Arguments

    tidy_vcf.

    -
    verbose
    +
    verbose

    (optional, logical) verbose = TRUE to be chatty during execution. Default: verbose = FALSE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution. Default: parallel.core = parallel::detectCores() - 1.

    @@ -108,9 +110,7 @@

    Arguments

    Value

    - - -

    A logical character string (TRUE/FALSE). That answer the question if +

    A logical character string (TRUE/FALSE). That answer the question if the data set is biallelic or not.

    @@ -130,15 +130,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/detect_biallelic_problems.html b/docs/reference/detect_biallelic_problems.html index fa11f77c..1f340ae8 100644 --- a/docs/reference/detect_biallelic_problems.html +++ b/docs/reference/detect_biallelic_problems.html @@ -7,7 +7,7 @@ - +
    @@ -38,7 +38,7 @@
    • - +
    @@ -89,7 +89,9 @@

    Detect biallelic problems

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. The tidy dataset needs a column with nucleotide information GT_VCF_NUC, @@ -98,13 +100,13 @@

    Arguments

    Look into radiator tidy_genomic_data.

    -
    verbose
    +
    verbose

    (optional, logical) verbose = TRUE to be chatty during execution. Default: verbose = TRUE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution. Default: parallel.core = parallel::detectCores() - 1.

    @@ -112,9 +114,7 @@

    Arguments

    Value

    - - -

    Several info

    +

    Several info

    Author

    @@ -133,15 +133,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/detect_dart_format.html b/docs/reference/detect_dart_format.html index 8fd774d3..9a27a5b1 100644 --- a/docs/reference/detect_dart_format.html +++ b/docs/reference/detect_dart_format.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    detect_dart_format

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/detect_duplicate_genomes.html b/docs/reference/detect_duplicate_genomes.html index 2d0c882f..98bec8f6 100644 --- a/docs/reference/detect_duplicate_genomes.html +++ b/docs/reference/detect_duplicate_genomes.html @@ -8,7 +8,7 @@ - +
    @@ -39,7 +39,7 @@
    • - +
    @@ -96,7 +96,9 @@

    Compute pairwise genome similarity or distance between individuals to highli

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -105,23 +107,23 @@

    Arguments

    tidy_vcf.

    -
    interactive.filter
    +
    interactive.filter

    (optional, logical) Do you want the filtering session to be interactive. Figures of distribution are shown before asking for filtering thresholds. Default: interactive.filter = TRUE.

    -
    detect.duplicate.genomes
    +
    detect.duplicate.genomes

    (optional, logical) For use inside radiator pipelines. Default: detect.duplicate.genomes = TRUE.

    -
    dup.threshold
    +
    dup.threshold

    Default: dup.threshold = 0. Turn off filter.

    -
    distance.method
    +
    distance.method

    (character) Depending on input data, 2 different methods are used (give similar results):

    • gds data The calculation is fast it's SNPRelate::snpgdsIBS under the hood.

      • @@ -133,7 +135,7 @@

      Arguments

      are tailored for biallelic and multiallelic markers.

    -
    genome
    +
    genome

    (logical) Computes pairwise genome similarity in parallel. The proportion of the shared genotypes is averaged across shared markers between each pairwise comparison. This method makes filtering easier because the @@ -142,7 +144,7 @@

    Arguments

    Default: genome = FALSE.

    -
    threshold.common.markers
    +
    threshold.common.markers

    (double, optional) When using the pairwise genome similarity approach (genome = TRUE), using a threshold will filter the pairwise comparison before generating the results. This is @@ -153,7 +155,7 @@

    Arguments

    Default: threshold.common.markers = NULL.

    -
    blacklist.duplicates
    +
    blacklist.duplicates

    (optional, logical) With blacklist.duplicates = TRUE, after visualization, the user is asked to enter a threshold to filter out duplicates. @@ -161,19 +163,19 @@

    Arguments

    interaction with user.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -181,9 +183,7 @@

    Arguments

    Value

    - - -

    A list with potentially 8 objects:

    • $distance : results of the distance method.

      • +

      A list with potentially 8 objects:

      • $distance : results of the distance method.

      • $distance.stats: Summary statistics of the distance method.

      • $pairwise.genome.similarity: results of the genome method.

      • $genome.stats: Summary statistics of the genome method.

        • @@ -231,7 +231,7 @@

        Author

        Examples

        - 
        if (FALSE) {
+    
        if (FALSE) { # \dontrun{
 # First run and simplest way (if you have the tidy tibble):
 dup <- radiator::detect_duplicate_genomes(data = "wombat_tidy.rad")
 
@@ -279,7 +279,7 @@ 
        Examples
        
 
 # Get the list of duplicates id
 dup.list.names <- data.frame(INDIVIDUALS = unique(c(dup.filtered$ID1, dup.filtered$ID2)))
-}
+} # }
        @@ -294,15 +294,15 @@

        Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/detect_genomic_format.html b/docs/reference/detect_genomic_format.html index e3829776..7bc94d1c 100644 --- a/docs/reference/detect_genomic_format.html +++ b/docs/reference/detect_genomic_format.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,7 +77,9 @@

    Used internally in radiator to detect the file format

    Arguments

    -
    data
    + + +
    data

    14 options for input: VCFs (SNPs or Haplotypes, to make the vcf population ready), plink (tped and bed), stacks haplotype file, genind (library(adegenet)), @@ -89,9 +91,7 @@

    Arguments

    Value

    - - -

    One of these file format:

    • tbl_df: for a data frame

      • +

      One of these file format:

      • tbl_df: for a data frame

      • genind: for a genind object

      • genlight: for a genlight object

      • gtypes: for a gtypes object

        • @@ -112,10 +112,10 @@

        Author

        Examples

        - 
        if (FALSE) {
+    
        if (FALSE) { # \dontrun{
 #To verify your file is detected by radiator as the correct format:
 radiator::detect_genomic_format(data = "populations.snps.vcf")
-}
+} # }
        @@ -130,15 +130,15 @@

        Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/detect_het_outliers.html b/docs/reference/detect_het_outliers.html index 7eb53d3b..49f4e887 100644 --- a/docs/reference/detect_het_outliers.html +++ b/docs/reference/detect_het_outliers.html @@ -7,7 +7,7 @@ - +
    @@ -38,7 +38,7 @@
    • - +
    @@ -93,7 +93,9 @@

    Detect heterozygotes outliers and estimate miscall rate

    Arguments

    -
    data
    + + +
    data

    14 options for input (diploid data only): VCFs (SNPs or Haplotypes, to make the vcf population ready), plink (tped, bed), stacks haplotype file, genind (library(adegenet)), @@ -109,12 +111,12 @@

    Arguments

    to understand it's limit before asking raditor to convert or filter your dataset.

    -
    nreps
    +
    nreps

    (integer, optional) The number of MCMC sweeps to do. Default: nreps = 2000.

    -
    burn.in
    +
    burn.in

    (integer, optional) The number of MCMC burn-in reps. With default, during execution, you will be asked to enter the nuber of burn-in. For this, a plot showing the heterozygote miscall rate for all @@ -125,14 +127,14 @@

    Arguments

    With default: burn.in = NULL.

    -
    strata
    +
    strata

    (path or object) The strata file or object. Additional documentation is available in read_strata. Use that function to whitelist/blacklist populations/individuals. Option to set pop.levels/pop.labels is also available.

    -
    filename
    +
    filename

    (optional, character) If !is.null(blacklist.id) || !is.null(pop.select), the modified strata is written by default in the working directory with date and time appended to strata_radiator_filtered, @@ -141,29 +143,25 @@

    Arguments

    Default: filename = NULL.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    ...
    +
    ...

    (optional) To pass further arguments for fine-tuning the function.

    Value

    - - -

    A folder generated automatically with date and time, +

    A folder generated automatically with date and time, the file het.summary.tsv contains the summary statistics. The file markers.genotypes.boundaries.pdf is the plot with boundaries. The overall genotyping and heterozygotes miscall rate is writen in the file overall_error_rate.tsv. The function also returns a list inside the global environment with 8 objects:

    - -

    1. input the input data, cleaned if filters were used during import.

    2. outlier.summary a list with a tibble and plot of genotypes frequencies and boundaries (also written in the folder).

      3. @@ -207,10 +205,10 @@

      Author

      Examples

      - 
      if (FALSE) {
+    
      if (FALSE) { # \dontrun{
 het.prob <- radiator::detect_het_outliers(
 data = "tuna.vcf", strata = "tuna.strata.tsv", nreps = 2000)
-}
+} # }
      @@ -225,15 +223,15 @@

      Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/detect_microsatellites.html b/docs/reference/detect_microsatellites.html index 2a7c706a..c3da3f6d 100644 --- a/docs/reference/detect_microsatellites.html +++ b/docs/reference/detect_microsatellites.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Detect microsatellites

    Arguments

    -
    data
    + + +
    data

    (path or object) Object in your global environment or a file in the working directory. The tibble must contain 2 columns named: MARKERS and SEQUENCE. @@ -91,7 +93,7 @@

    Arguments

    automatically this file under the name whitelist.markers.tsv.

    -
    gmata.dir
    +
    gmata.dir

    (path) For the function to work, the path to the directory with GMATA software needs to be given. If not found or NULL, the function download GMATA @@ -99,7 +101,7 @@

    Arguments

    Default: gmata.path = NULL.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -107,9 +109,7 @@

    Arguments

    Value

    - - -

    6 files are returned in the folder: detect_microsatellites:

    1. ".fa.fms": the fasta file of sequences

      2. +

      6 files are returned in the folder: detect_microsatellites:

      1. ".fa.fms": the fasta file of sequences

      2. ".fa.fms.sat1": the summary of sequences analysed (not important)

      3. ".fa.ssr": The microsatellites found per markers (see GMATA doc)

      4. ".fa.ssr.sat2": Extensive summary (see GMATA doc).

        5. @@ -130,7 +130,7 @@

        Author

        Examples

        - 
        if (FALSE) {
+    
        if (FALSE) { # \dontrun{
 # The simplest way to run the function when the raw data was DArT:
 mic <- radiator::detect_microsatellites(data = "my_whitelist.tsv")
 
@@ -160,7 +160,7 @@ 
        Examples
        
 #   return(fasta)
 #  } #prep_stacks_fasta
 
-}
+} # }
        @@ -175,15 +175,15 @@

        Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/detect_mixed_genomes.html b/docs/reference/detect_mixed_genomes.html index 6d0820e6..458e0dc5 100644 --- a/docs/reference/detect_mixed_genomes.html +++ b/docs/reference/detect_mixed_genomes.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -90,7 +90,9 @@

    Detect mixed genomes

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -99,19 +101,19 @@

    Arguments

    tidy_vcf.

    -
    interactive.filter
    +
    interactive.filter

    (optional, logical) Do you want the filtering session to be interactive. Figures of distribution are shown before asking for filtering thresholds. Default: interactive.filter = TRUE.

    -
    detect.mixed.genomes
    +
    detect.mixed.genomes

    (optional, logical) For use inside radiator pipelines. Default: detect.mixed.genomes = TRUE.

    -
    ind.heterozygosity.threshold
    +
    ind.heterozygosity.threshold

    (string, double, optional) Blacklist individuals based on observed heterozygosity (averaged across markers).

    @@ -124,7 +126,7 @@

    Arguments

    the filter and the function will only output the plots and table of heterozygosity.

    -
    by.strata
    +
    by.strata

    (optional, logical) Can only be used when interactive.filter = TRUE, allows to enter heterozygosity thresholds by strata, instead of overall. This is not recommended @@ -133,19 +135,19 @@

    Arguments

    Default: by.strata = FALSE.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -153,12 +155,8 @@

    Arguments

    Value

    - - -

    The function returns inside the global environment a list with +

    The function returns inside the global environment a list with 5 objects:

    - -

    1. the individual's heterozigosity ($individual.heterozygosity) a dataframe containing for each individual, the population id, the number of genotyped markers, the number of missing genotypes (based on the number of @@ -215,7 +213,7 @@

      Author

      Examples

      - 
      if (FALSE) {
+    
      if (FALSE) { # \dontrun{
 #Step1: highlight outlier individuals, the simplest way to run:
 
 data <- radiator::detect_mixed_genomes(data = "wombat_tidy.rad")
@@ -229,7 +227,7 @@ 
      Examples
      
     ) %>%
 radiator::detect_mixed_genomes(.)
 
-}
+} # }
      @@ -244,15 +242,15 @@

      Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/detect_paralogs.html b/docs/reference/detect_paralogs.html index 17609ea2..c0b60531 100644 --- a/docs/reference/detect_paralogs.html +++ b/docs/reference/detect_paralogs.html @@ -8,7 +8,7 @@ - +
    @@ -39,7 +39,7 @@
    • - +
    @@ -92,7 +92,9 @@

    Detect paralogs

    Arguments

    -
    data
    + + +
    data

    (2 options) A Genomic Data Structure (GDS) file or object generated by radiator.

    How to get GDS data ? @@ -101,19 +103,19 @@

    Arguments

    tidy_vcf.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -121,13 +123,9 @@

    Arguments

    Value

    - - -

    The function returns the GDS data inside the global environment. +

    The function returns the GDS data inside the global environment. In the directory generated with detect_paralogs in it, the function writes a tibble with the summary and the HD plot.

    - -

    The tibble as 1 line per SNPs/MARKERS and columns are:

    • VARIANT_ID: the GDS SNP id, to have all the markers metadata use extract_markers_metadata.

    • NUMBER_HET: the number of heterozygote genotype.

      • @@ -144,7 +142,7 @@

      Value

    Assumptions/Prerequisites

    - +

    1. read the paper: Read Garrett McKinney @@ -196,7 +194,7 @@

      Author

      Examples

      - 
      if (FALSE) {
+    
      if (FALSE) { # \dontrun{
 # require(httr)
 # using the Chinook VCF dataset in dryad, from McKinney et al. 2017 paper:
 writeBin(object = httr::content(x = httr::GET(
@@ -207,7 +205,7 @@ 
      Examples
      
 # Import VCF and run the function
 chinook.paralogs <- radiator::read_vcf(data = "chinook.vcf", vcf.stats = FALSE) %>%
     radiator::detect_paralogs(data = .)
-}
+} # }
      @@ -222,15 +220,15 @@

      Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/detect_ref_genome.html b/docs/reference/detect_ref_genome.html index 8376ba98..83e19f24 100644 --- a/docs/reference/detect_ref_genome.html +++ b/docs/reference/detect_ref_genome.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,12 +77,14 @@

    Detect reference genome

    Arguments

    -
    chromosome
    + + +
    chromosome

    (string) String with chromosome ID, unique or not. Default: chromosome = NULL.

    -
    data
    +
    data

    (optional, path or object) radiator GDS object or file. When this argument is used, the function look inside the GDS radiator node for:

    • reference.genome node and TRUE/FALSE value

    • markers.meta node and detect the information using the CHROM @@ -91,7 +93,7 @@

      Arguments

    Default: data = NULL.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -99,9 +101,7 @@

    Arguments

    Value

    - - -

    TRUE/FALSE if dataset is assembled with a reference genome or not.

    +

    TRUE/FALSE if dataset is assembled with a reference genome or not.

    Author

    @@ -110,9 +110,9 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 ref.genome <- radiator::detect_ref_genome(chromosome = tidy.data$CHROM)
-}
+} # }
    @@ -127,15 +127,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/diagnostic_maf.html b/docs/reference/diagnostic_maf.html index 915fd234..b4c79b24 100644 --- a/docs/reference/diagnostic_maf.html +++ b/docs/reference/diagnostic_maf.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,7 +77,9 @@

    MA diagnostic

    Arguments

    -
    data
    + + +
    data

    A file in the working directory or object in the global environment in wide or long (tidy) formats. To import, the function uses radiator @@ -85,11 +87,11 @@

    Arguments

    See details of this function for more info.

    -
    group.rank
    +
    group.rank

    (Number) The number of group to class the MAF.

    -
    filename
    +
    filename

    (optional) Name of the file written to the working directory.

    @@ -104,10 +106,10 @@

    See also

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 problem <- radiator::diagnostic_ma(
 data = tidy.salmon.data, group.rank = 10)
-}
+} # }
    @@ -122,15 +124,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/distance2tibble.html b/docs/reference/distance2tibble.html index 98ccaeb0..b14ef465 100644 --- a/docs/reference/distance2tibble.html +++ b/docs/reference/distance2tibble.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -96,15 +96,15 @@

    distance2tibble

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/distance_individuals.html b/docs/reference/distance_individuals.html index a69729f0..a59c8342 100644 --- a/docs/reference/distance_individuals.html +++ b/docs/reference/distance_individuals.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -93,15 +93,15 @@

    Distance individuals

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/erase_genotypes.html b/docs/reference/erase_genotypes.html index 5f4fc712..6d7ce06f 100644 --- a/docs/reference/erase_genotypes.html +++ b/docs/reference/erase_genotypes.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -90,38 +90,38 @@

    Erase genotypes

    Arguments

    -
    tidy.vcf.file
    + + +
    tidy.vcf.file

    A data frame object or file (using ".tsv") of a tidy vcf.

    -
    haplotypes.file
    +
    haplotypes.file

    (optional) The 'batch_x.haplotypes.tsv'. If you want to erase the genotypes that don't pass the threshold.

    -
    read.depth.threshold
    +
    read.depth.threshold

    (integer) Threshold for the read depth.

    -
    allele.depth.threshold
    +
    allele.depth.threshold

    (integer) Threhold for the min depth of REF or ALT alleles.

    -
    allele.imbalance.threshold
    +
    allele.imbalance.threshold

    (numeric) Threshold of ratio between ALT and REF depth of coverage. See details below.

    -
    filename
    +
    filename

    (optional) Name of the file written to the working directory.

    Value

    - - -

    The function returns the blacklisted individuals genotypes, +

    The function returns the blacklisted individuals genotypes, by loci, position (SNP, POS in stacks), populations and individuals. For VCF, return the tidy vcf in the global environment only and in the directory with filename. For haplotype file the original @@ -154,15 +154,15 @@

    Details

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/estimate_m.html b/docs/reference/estimate_m.html index fb0a9590..5be9935e 100644 --- a/docs/reference/estimate_m.html +++ b/docs/reference/estimate_m.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -84,28 +84,30 @@

    heterozygotes miscall rate

    Arguments

    -
    data
    + + +
    data

    A tidy data frame (biallelic only).

    -
    nreps
    +
    nreps

    number of MCMC sweeps to do. Default: nreps = 200.

    -
    m_init
    +
    m_init

    initial starting value for m must be between 0 and 1

    -
    a0
    +
    a0

    beta parameter for reference alleles

    -
    a1
    +
    a1

    beta parameter for alternate alleles

    -
    sm
    +
    sm

    standard devation of proposal distribution for m

    @@ -126,15 +128,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/extract_coverage.html b/docs/reference/extract_coverage.html index b9f7cc2d..1985989b 100644 --- a/docs/reference/extract_coverage.html +++ b/docs/reference/extract_coverage.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -98,62 +98,64 @@

    check_coverage

    Arguments

    -
    gds
    + + +
    gds

    The gds object.

    -
    genotypes.metadata.check
    +
    genotypes.metadata.check

    (optional, logical) Look for already extracted coverage information in the radiator genotypes_metadata field of the GDS. Default: genotypes.metadata.check = FALSE.

    -
    stacks.haplo.check
    +
    stacks.haplo.check

    (optional, logical) stacks haplotypes VCF header is baddly generated. It will say you have Read and allele Depth info, but you don't. Default: stacks.haplo.check = FALSE.

    -
    dart.check
    +
    dart.check

    (optional, logical) DArT have different reporting for coverage information. Will no longer report the average coverage stats from 1 and 2-rows DArT format. Default: dart.check = FALSE.

    -
    individuals
    +
    individuals

    (optional, logical) Default: individuals = TRUE.

    -
    markers
    +
    markers

    (optional, logical) Default: markers = TRUE.

    -
    dp
    +
    dp

    (optional, logical) Default: dp = TRUE.

    -
    ad
    +
    ad

    (optional, logical) Default: ad = TRUE.

    -
    coverage.stats
    +
    coverage.stats

    (optional, character string). Choice of stats to use with coverage. Default: coverage.stats = c("sum", "mean", "median", "iqr").

    -
    subsample.info
    +
    subsample.info

    (optional, double) Default: subsample.info = 1. The subsample proportion used (e.g. 0.3 or none the default).

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    @@ -172,15 +174,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/extract_dart_target_id.html b/docs/reference/extract_dart_target_id.html index 06366fd6..4f186615 100644 --- a/docs/reference/extract_dart_target_id.html +++ b/docs/reference/extract_dart_target_id.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -81,7 +81,9 @@

    Extract DArT<

    Arguments

    -
    data
    + + +
    data

    One of the DArT output files. 6 formats used by DArT are recognized by radiator. recognised:

    1. 1row: Genotypes are in 1 row and coded (0, 1, 2, -). @@ -106,22 +108,16 @@

      Arguments

      the function.

    -
    write
    +
    write

    With default write = TRUE, the dart target id column is written in a file in the working directory.

    Value

    - - -

    A tidy dataframe with a TARGET_ID column. For cleaning, the TARGET_ID

    - - -

    column is treated like the column INDIVIDUALS. Spaces and ,

    - - -

    are removed, _ and : are changed to a dash - and +

    A tidy dataframe with a TARGET_ID column. For cleaning, the TARGET_ID +column is treated like the column INDIVIDUALS. Spaces and , +are removed, _ and : are changed to a dash - and UPPER case is used. see cleaning doc for logic behind this.

    @@ -132,7 +128,7 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # Built a strata file:
 strata <- radiator::extract_dart_target_id("mt.dart.file.csv") %>%
     dplyr::mutate(
@@ -140,7 +136,7 @@ 
    Examples
    
         STRATA = "fill this"
     ) %>%
     readr::write_tsv(x = ., file = "my.new.dart.strata.tsv")
-}
+} # }
    @@ -155,15 +151,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/extract_data_source.html b/docs/reference/extract_data_source.html index 7dc8faee..3d8e8b01 100644 --- a/docs/reference/extract_data_source.html +++ b/docs/reference/extract_data_source.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    extract_data_source

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/extract_dots.html b/docs/reference/extract_dots.html index fd0bcd1e..bdae56d8 100644 --- a/docs/reference/extract_dots.html +++ b/docs/reference/extract_dots.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    extract_dots

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/extract_genotypes_metadata.html b/docs/reference/extract_genotypes_metadata.html index 7aa9273e..46bf706a 100644 --- a/docs/reference/extract_genotypes_metadata.html +++ b/docs/reference/extract_genotypes_metadata.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -87,39 +87,41 @@

    extract_genotypes_metadata

    Arguments

    -
    gds
    + + +
    gds

    The gds object.

    -
    genotypes.meta.select
    +
    genotypes.meta.select

    (optional, character) Default:genotypes.meta.select = NULL.

    -
    genotypes
    +
    genotypes

    (optional, character) Default: genotypes = FALSE.

    -
    radiator.node
    +
    radiator.node

    (optional, logical) Default: radiator.node = TRUE.

    -
    index.only
    +
    index.only

    (optional, logical) Default: index.only = FALSE.

    -
    sync.markers.individuals
    +
    sync.markers.individuals

    (optional, logical) Default: sync.markers.individuals = TRUE.

    -
    whitelist
    +
    whitelist

    (optional, logical) Default: whitelist = FALSE.

    -
    blacklist
    +
    blacklist

    (optional, logical) Default: blacklist = FALSE.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -138,15 +140,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/extract_individuals_metadata.html b/docs/reference/extract_individuals_metadata.html index fe976fb9..5cc60de4 100644 --- a/docs/reference/extract_individuals_metadata.html +++ b/docs/reference/extract_individuals_metadata.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -84,27 +84,29 @@

    extract_individuals_metadata

    Arguments

    -
    gds
    + + +
    gds

    The gds object.

    -
    ind.field.select
    +
    ind.field.select

    (optional, character) Default:ind.field.select = NULL.

    -
    radiator.node
    +
    radiator.node

    (optional, logical) Default:radiator.node = TRUE.

    -
    whitelist
    +
    whitelist

    (optional, logical) Default:whitelist = FALSE.

    -
    blacklist
    +
    blacklist

    (optional, logical) Default:blacklist = FALSE.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -123,15 +125,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/extract_individuals_vcf.html b/docs/reference/extract_individuals_vcf.html index d04c486a..dd2a718a 100644 --- a/docs/reference/extract_individuals_vcf.html +++ b/docs/reference/extract_individuals_vcf.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -81,15 +81,15 @@

    Extract individuals from vcf file

    Arguments

    -
    vcf
    + + +
    vcf

    (character, path) The path to the vcf file.

    Value

    - - -

    A tibble with a column: INDIVIDUALS.

    +

    A tibble with a column: INDIVIDUALS.

    See also

    @@ -102,12 +102,12 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # Built a strata file:
 strata <- radiator::extract_individuals_vcf("my.vcf") %>%
     dplyr::mutate(STRATA = "fill this") %>%
     readr::write_tsv(x = ., file = "my.new.vcf.strata.tsv")
-}
+} # }
    @@ -122,15 +122,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/extract_info_vcf.html b/docs/reference/extract_info_vcf.html index 8de76c91..bbc31f6a 100644 --- a/docs/reference/extract_info_vcf.html +++ b/docs/reference/extract_info_vcf.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    extract_info_vcf

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/extract_markers_metadata.html b/docs/reference/extract_markers_metadata.html index 1f8a248a..47004523 100644 --- a/docs/reference/extract_markers_metadata.html +++ b/docs/reference/extract_markers_metadata.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -84,27 +84,29 @@

    extract_markers_metadata

    Arguments

    -
    gds
    + + +
    gds

    The gds object.

    -
    markers.meta.select
    +
    markers.meta.select

    (optional, character) Default:markers.meta.select = NULL.

    -
    radiator.node
    +
    radiator.node

    (optional, logical) Default:radiator.node = TRUE.

    -
    whitelist
    +
    whitelist

    (optional, logical) Default:whitelist = FALSE.

    -
    blacklist
    +
    blacklist

    (optional, logical) Default:blacklist = FALSE.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -123,15 +125,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_blacklist_genotypes.html b/docs/reference/filter_blacklist_genotypes.html index b3ed14f2..f21ba6f9 100644 --- a/docs/reference/filter_blacklist_genotypes.html +++ b/docs/reference/filter_blacklist_genotypes.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Filter dataset with blacklist of genotypes

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -92,7 +94,7 @@

    Arguments

    tidy_vcf.

    -
    blacklist.genotypes
    +
    blacklist.genotypes

    (path or object) The blacklist is an object in your global environment or a file in the working directory (e.g. "blacklist.geno.tsv"). @@ -106,13 +108,13 @@

    Arguments

    Default blacklist.genotypes = NULL.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -120,7 +122,7 @@

    Arguments

    Life cycle

    - +

    This function arguments will be subject to changes. Currently the function uses @@ -135,11 +137,11 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 data <- radiator::filter_blacklist_genotypes(
     data = data, blacklist.geno = "blacklist.geno.tsv"
     )
-}
+} # }
    @@ -154,15 +156,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_common_markers.html b/docs/reference/filter_common_markers.html index 4061c425..076ac7ae 100644 --- a/docs/reference/filter_common_markers.html +++ b/docs/reference/filter_common_markers.html @@ -10,7 +10,7 @@ - +
    @@ -41,7 +41,7 @@
    • - +
    @@ -98,7 +98,9 @@

    Filter common markers between strata

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -107,40 +109,38 @@

    Arguments

    tidy_vcf.

    -
    filter.common.markers
    +
    filter.common.markers

    (optional, logical) Default: filter.common.markers = TRUE.

    -
    fig
    +
    fig

    (optional, logical) fig = TRUE will produce an UpSet fig to visualize the number of markers between populations. The package is required for this to work... Default: fig = FALSE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) verbose = TRUE to be chatty during execution. Default: verbose = FALSE.

    -
    ...
    +
    ...

    (optional) To pass further arguments for fine-tuning the function and legacy arguments.

    Value

    - - -

    A list with the filtered input, whitelist and blacklist of markers..

    +

    A list with the filtered input, whitelist and blacklist of markers..

    Author

    @@ -149,10 +149,10 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 require(SeqArray) # when using gds
 common <- radiator::filter_common_markers(data = "my.radiator.gds.rad", verbose = TRUE)
-}
+} # }
    @@ -167,15 +167,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_coverage.html b/docs/reference/filter_coverage.html index 69113610..4568cf3f 100644 --- a/docs/reference/filter_coverage.html +++ b/docs/reference/filter_coverage.html @@ -7,7 +7,7 @@ - +
    @@ -38,7 +38,7 @@
    • - +
    @@ -93,7 +93,9 @@

    Filter markers mean coverage

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -102,14 +104,14 @@

    Arguments

    tidy_vcf.

    -
    interactive.filter
    +
    interactive.filter

    (optional, logical) Do you want the filtering session to be interactive. Figures of distribution are shown before asking for filtering thresholds. Default: interactive.filter = TRUE.

    -
    filter.coverage
    +
    filter.coverage

    (optional, string) 2 options:

    • character string filter.coverage = "outliers" will use as thresholds the lower and higher outlier values in the box plot.

    • integers string filter.coverage = c(10, 200). For the @@ -117,24 +119,24 @@

      Arguments

    Default: filter.coverage = NULL.

    -
    filename
    +
    filename

    (optional, character) Default: filename = NULL.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -142,9 +144,7 @@

    Arguments

    Value

    - - -

    With interactive.filter = FALSE, a list in the global environment, +

    With interactive.filter = FALSE, a list in the global environment, with 7 objects:

    1. $tidy.filtered.mac

    2. $whitelist.markers

    3. $blacklist.markers

      4. @@ -157,7 +157,7 @@

      Value

    Advance mode

    - +

    dots-dots-dots ... allows to pass several arguments for fine-tuning the function:

    1. filter.common.markers (optional, logical). @@ -174,7 +174,7 @@

      Advance mode

    Interactive version

    - +

    To help choose a threshold for the local and global MAF @@ -190,9 +190,9 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # The minumum
-}
+} # }
    @@ -207,15 +207,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_dart_reproducibility.html b/docs/reference/filter_dart_reproducibility.html index 740bb150..e01dfcc0 100644 --- a/docs/reference/filter_dart_reproducibility.html +++ b/docs/reference/filter_dart_reproducibility.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -90,7 +90,9 @@

    Filter data based on DArT reproducibility statistics

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -99,14 +101,14 @@

    Arguments

    tidy_vcf.

    -
    interactive.filter
    +
    interactive.filter

    (optional, logical) Do you want the filtering session to be interactive. Figures of distribution are shown before asking for filtering thresholds. Default: interactive.filter = TRUE.

    -
    filter.reproducibility
    +
    filter.reproducibility

    (double, character) This is best decided after viewing the figures. Usually values higher than 0.95 are not uncommon. The value can also be character: filter.reproducibility = "outliers". @@ -114,19 +116,19 @@

    Arguments

    Default: filter.reproducibility = NULL.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -134,9 +136,7 @@

    Arguments

    Value

    - - -

    A list in the global environment with 6 objects:

    1. $whitelist.markers

      2. +

      A list in the global environment with 6 objects:

      1. $whitelist.markers

      2. $blacklist.markers

      3. $filters.parameters

      The object can be isolated in separate object outside the list by @@ -153,7 +153,7 @@

      Details

      Examples

      - 
      if (FALSE) {
+    
      if (FALSE) { # \dontrun{
 spotted.cod <- radiator::read_dart(
     data = "Combined_1514and1614_SNP_80Callrate.csv",
     strata = "strata.dart.spotted.cod.tsv"
@@ -162,7 +162,7 @@ 
      Examples
      
     data = spotted.cod,
     filter.reproducibility = 0.97
 )
-}
+} # }
      @@ -177,15 +177,15 @@

      Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_fis.html b/docs/reference/filter_fis.html index 2c8d1bb7..49a38db9 100644 --- a/docs/reference/filter_fis.html +++ b/docs/reference/filter_fis.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -86,7 +86,9 @@

    Fis filter

    Arguments

    -
    data
    + + +
    data

    14 options for input (diploid data only): VCFs (SNPs or Haplotypes, to make the vcf population ready), plink (tped, bed), stacks haplotype file, genind (library(adegenet)), @@ -102,33 +104,33 @@

    Arguments

    to understand it's limit before asking raditor to convert or filter your dataset.

    -
    approach
    +
    approach

    Character. By "SNP" or by "haplotype". The function will consider the SNP or haplotype statistics to filter the marker. Default by "haplotype".

    -
    fis.min.threshold
    +
    fis.min.threshold

    Number.

    -
    fis.max.threshold
    +
    fis.max.threshold

    Number.

    -
    fis.diff.threshold
    +
    fis.diff.threshold

    Number (0 - 1)

    -
    pop.threshold
    +
    pop.threshold

    Fixed number of pop required to keep the locus.

    -
    percent
    +
    percent

    Is the threshold a percentage ? TRUE or FALSE.

    -
    filename
    +
    filename

    (optional) The function uses write.fst, to write the tidy data frame in the folder created in the working directory. The file extension appended to @@ -162,15 +164,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_genotyping.html b/docs/reference/filter_genotyping.html index 2598e08d..2a263c0b 100644 --- a/docs/reference/filter_genotyping.html +++ b/docs/reference/filter_genotyping.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -91,7 +91,9 @@

    Filter markers based on genotyping/missing rate

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -100,37 +102,37 @@

    Arguments

    tidy_vcf.

    -
    interactive.filter
    +
    interactive.filter

    (optional, logical) Do you want the filtering session to be interactive. With default: interactive.filter == TRUE, figures and tables are shown before making decisions for filtering.

    -
    filter.genotyping
    +
    filter.genotyping

    (optional, string) 2 options:

    • character string filter.genotyping = "outliers" will use as thresholds the higher outlier values in the box plot.

    • double filter.genotyping = 0.2. Will allow up to 0.2 missing genotypes.

    Default: filter.genotyping = NULL.

    -
    filename
    +
    filename

    (optional, character) Default: filename = NULL.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -138,9 +140,7 @@

    Arguments

    Value

    - - -

    With interactive.filter = FALSE, a list in the global environment, +

    With interactive.filter = FALSE, a list in the global environment, with 7 objects:

    1. $tidy.filtered.mac

    2. $whitelist.markers

    3. $blacklist.markers

      4. @@ -153,7 +153,7 @@

      Value

    Advance mode

    - +

    dots-dots-dots ... allows to pass several arguments for fine-tuning the function:

    1. filter.common.markers (optional, logical). @@ -170,7 +170,7 @@

      Advance mode

    Interactive version

    - +

    To help choose a threshold use the interactive version.

    @@ -185,9 +185,9 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # The minumum
-}
+} # }
    @@ -202,15 +202,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_het.html b/docs/reference/filter_het.html index 97efdfe0..825fd92a 100644 --- a/docs/reference/filter_het.html +++ b/docs/reference/filter_het.html @@ -23,7 +23,7 @@ - +
    @@ -54,7 +54,7 @@
    • - +
    @@ -128,14 +128,16 @@

    Heterozygosity filter

    Arguments

    -
    interactive.filter
    + + +
    interactive.filter

    (optional, logical) Do you want the filtering session to be interactive. With the default, the user is asked to see figures of distribution before making decisions for filtering with heterozygosity statistics. Default: interactive.filter == TRUE.

    -
    data
    +
    data

    14 options for input (diploid data only): VCFs (SNPs or Haplotypes, to make the vcf population ready), plink (tped, bed), stacks haplotype file, genind (library(adegenet)), @@ -151,7 +153,7 @@

    Arguments

    to understand it's limit before asking raditor to convert or filter your dataset.

    -
    strata
    +
    strata

    (optional) The strata file is a tab delimited file with a minimum of 2 columns headers: INDIVIDUALS and STRATA. Documented in read_strata. @@ -161,7 +163,7 @@

    Arguments

    Default: strata = NULL.

    -
    ind.heterozygosity.threshold
    +
    ind.heterozygosity.threshold

    (string, double, optional) Blacklist individuals based on observed heterozygosity (averaged across markers).

    @@ -174,7 +176,7 @@

    Arguments

    the filter and the function will only output the plots and table of heterozygosity.

    -
    het.approach
    +
    het.approach

    (Character string). First value, "SNP" or "haplotype". The haplotype approach considers the statistic consistency on the read (locus/haplotype). The major difference: @@ -186,14 +188,14 @@

    Arguments

    Default: het.approach = c("SNP", "overall").

    -
    het.threshold
    +
    het.threshold

    Number Biallelic markers usually max 0.5. But departure from this value is common. The higher the proportion threshold, the more relaxed the filter is. With default there is no filtering. Default: het.threshold = 1.

    -
    het.dif.threshold
    +
    het.dif.threshold

    Number (0 - 1). For het.approach = "haplotype" only. You can set a threshold for the difference in het along your read. Set the number your willing to tolerate on the same read/haplotype. @@ -205,7 +207,7 @@

    Arguments

    Default: het.dif.threshold = 1.

    -
    outlier.pop.threshold
    +
    outlier.pop.threshold

    (integer, optional) Useful to incorporate problematic populations dragging down polymorphism discovery, but still wanted for analysis. Use this threshold to allow variance in the number of populations passing @@ -218,7 +220,7 @@

    Arguments

    Default: outlier.pop.threshold = 1. See details for more info.

    -
    helper.tables
    +
    helper.tables

    (logical) Output tables that show the number of markers blacklisted or whitelisted based on a series of automatic thresholds to guide decisions. When interactive.filter == TRUE, @@ -226,7 +228,7 @@

    Arguments

    Default: helper.tables = FALSE.

    -
    coverage.info
    +
    coverage.info

    (optional, logical) Use coverage.info = TRUE, if you want to visualize the relationshio between locus coverage and locus observed heterozygosity @@ -234,7 +236,7 @@

    Arguments

    Default: coverage.info = FALSE.

    -
    filename
    +
    filename

    (optional) The function uses write.fst, to write the tidy data frame in the folder created in the working directory. The file extension appended to @@ -242,24 +244,20 @@

    Arguments

    Default: filename = NULL.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    ...
    +
    ...

    (optional) To pass further arguments for fine-tuning the function.

    Value

    - - -

    The function returns inside the global environment a list with +

    The function returns inside the global environment a list with 15 objects, the objects names are found by using names(your.list.name):

    - -

    1. filtered tidy data frame: $tidy.filtered.het

    2. whitelist of markers:$whitelist.markers

    3. the strata:$strata

      4. @@ -345,15 +343,15 @@

      See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_hwe.html b/docs/reference/filter_hwe.html index dddcfd84..9ddf2569 100644 --- a/docs/reference/filter_hwe.html +++ b/docs/reference/filter_hwe.html @@ -21,7 +21,7 @@ - +
    @@ -52,7 +52,7 @@
    • - +
    @@ -124,26 +124,28 @@

    Filter markers based on Hardy-Weinberg Equilibrium

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    interactive.filter
    +
    interactive.filter

    (optional, logical) Do you want the filtering session to be interactive. Figures of distribution are shown before asking for filtering thresholds. Default: interactive.filter = TRUE.

    -
    filter.hwe
    +
    filter.hwe

    (optional, logical) Used inside radiator pipeline. Default: filter.hwe = TRUE.

    -
    strata
    +
    strata

    (optional) The strata file is a tab delimited file with a minimum of 2 columns headers: INDIVIDUALS and STRATA. Documented in read_strata. @@ -153,7 +155,7 @@

    Arguments

    Default: strata = NULL.

    -
    hw.pop.threshold
    +
    hw.pop.threshold

    (integer, optional) Remove markers that have a certain number of pops in Hardy-Weinberg disequilibrium. @@ -162,7 +164,7 @@

    Arguments

    Default: hw.pop.threshold = NULL.

    -
    midp.threshold
    +
    midp.threshold

    (integer, optional) By default the function generates blacklists/whitelists of markers and filtered tidy datasets for the 5 mid p-value. @@ -178,7 +180,7 @@

    Arguments

    Default: midp.threshold = 4.

    -
    filename
    +
    filename

    (optional) The function uses write.fst, to write the tidy data frame in the folder created in the working directory. The file extension appended to @@ -186,19 +188,19 @@

    Arguments

    Default: filename = NULL.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -206,9 +208,7 @@

    Arguments

    Value

    - - -

    A list in the global environment objects:

    1. $path.folder: the path to the folder generated.

      2. +

      A list in the global environment objects:

      1. $path.folder: the path to the folder generated.

      2. $hw.pop.threshold: the number of populations tolerated to be in HWD before blacklisting the markers.

      3. $plot.hwd.thresholds: useful figure that highlight the number of markers @@ -336,7 +336,7 @@

        References

        Examples

        - 
        if (FALSE) {
+    
        if (FALSE) { # \dontrun{
 require(HardyWeinberg)
 library(radiator)
 # for the interactive version (recommended)
@@ -345,7 +345,7 @@ 
        Examples
        
    strata = "turtle.strata.tsv",
    filename = "hwe.turtle"
 )
-}
+} # }
        @@ -360,15 +360,15 @@

        Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_individuals.html b/docs/reference/filter_individuals.html index 9ee1f4dd..c7ece8ee 100644 --- a/docs/reference/filter_individuals.html +++ b/docs/reference/filter_individuals.html @@ -12,7 +12,7 @@ - +
    @@ -43,7 +43,7 @@
    • - +
    @@ -103,7 +103,9 @@

    Filter individuals based on genotyping/missingness rate, heterozygosity and

    Arguments

    -
    data
    + + +
    data

    (2 options) A Genomic Data Structure (GDS) file or object generated by radiator.

    How to get GDS? @@ -112,26 +114,26 @@

    Arguments

    tidy_vcf.

    -
    interactive.filter
    +
    interactive.filter

    (optional, logical) Do you want the filtering session to be interactive. Figures of distribution are shown before asking for filtering thresholds. Default: interactive.filter = TRUE.

    -
    filter.individuals.missing
    +
    filter.individuals.missing

    (optional, double) A proportion above which the individuals are blacklisted and removed from the dataset. Default: filter.individuals.missing = NULL.

    -
    filter.individuals.heterozygosity
    +
    filter.individuals.heterozygosity

    (optional, string of doubles) A proportion below and above which the individuals are blacklisted and removed from the dataset. Default: filter.individuals.heterozygosity = NULL.

    -
    filter.individuals.coverage.total
    +
    filter.individuals.coverage.total

    (optional, string of doubles) Target the total coverage per samples. A proportion below and @@ -139,33 +141,33 @@

    Arguments

    Default: filter.individuals.coverage.total = NULL.

    -
    filter.individuals.coverage.median
    +
    filter.individuals.coverage.median

    (optional, string of integers) Target the median coverage per samples. Integers, below and above, that blacklist individuals (removed from the dataset) Default: filter.individuals.coverage.median = NULL.

    -
    filter.individuals.coverage.iqr
    +
    filter.individuals.coverage.iqr

    (optional, string of integers) Target the IQR (Interquartile Range) coverage per samples. Integers, below and above, that blacklist individuals (removed from the dataset) Default: filter.individuals.coverage.iqr = NULL.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -173,9 +175,7 @@

    Arguments

    Value

    - - -

    A list with the filtered input and blacklist of individuals.

    +

    A list with the filtered input and blacklist of individuals.

    See also

    @@ -190,7 +190,7 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 require(SeqArray)
 
 # blacklisting outliers individuals:
@@ -207,7 +207,7 @@ 
    Examples
    
     filter.individuals.heterozygosity = c(0.02, 0.03),
     filter.individuals.coverage.total = c(900000, 5000000))
 
-}
+} # }
    @@ -222,15 +222,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_ld.html b/docs/reference/filter_ld.html index 4f8fe3ee..1d16e470 100644 --- a/docs/reference/filter_ld.html +++ b/docs/reference/filter_ld.html @@ -23,7 +23,7 @@ - +
    @@ -54,7 +54,7 @@
    • - +
    @@ -122,7 +122,9 @@

    GBS/RADseq short and long distance linkage disequilibrium pruning

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -131,14 +133,14 @@

    Arguments

    tidy_vcf.

    -
    interactive.filter
    +
    interactive.filter

    (optional, logical) Do you want the filtering session to be interactive. Figures of distribution are shown before asking for filtering thresholds. Default: interactive.filter = TRUE.

    -
    filter.short.ld
    +
    filter.short.ld

    (character) 5 options (default: filter.short.ld = "mac"):

    1. filter.short.ld = "random" for a random selection of 1 SNP on the read,

    2. filter.short.ld = "first" for the first one on the read...,

    3. filter.short.ld = "last" for the last SNP on the read and

      4. @@ -152,32 +154,32 @@

      Arguments

    -
    filter.long.ld
    +
    filter.long.ld

    (optional, double) The threshold to prune SNP based on Long Distance Linkage Disequilibrium. The argument filter.long.ld is the absolute value of measurement. Default: filter.long.ld = NULL.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    filename
    +
    filename

    (optional, character) File name prefix for file written in the working directory. Default: filename = NULL.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -185,9 +187,7 @@

    Arguments

    Value

    - - -

    A list in the global environment, with these objects:

    1. $ld.summary: tibble with LD statistics used for the boxplot

      2. +

      A list in the global environment, with these objects:

      1. $ld.summary: tibble with LD statistics used for the boxplot

      2. $ld.boxplot: box plot of LD values

      3. $whitelist.ld: whitelist of markers kept after filtering for LD. The argument filter.long.ld must be used to generate the whitelist.

        4. @@ -251,7 +251,7 @@

        Author

        Examples

        - 
        if (FALSE) {
+    
        if (FALSE) { # \dontrun{
 require(SNPRelate)
 #To install SNPRelate:
 install.packages("BiocManager")
@@ -276,7 +276,7 @@ 
        Examples
        
          long.ld.missing = TRUE)
 
 
-}
+} # }
        @@ -291,15 +291,15 @@

        Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_monomorphic.html b/docs/reference/filter_monomorphic.html index 42dcb9a9..5c46af70 100644 --- a/docs/reference/filter_monomorphic.html +++ b/docs/reference/filter_monomorphic.html @@ -15,7 +15,7 @@ - +
    @@ -46,7 +46,7 @@
    • - +
    @@ -104,7 +104,9 @@

    Filter monomorphic markers

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -113,24 +115,24 @@

    Arguments

    tidy_vcf.

    -
    filter.monomorphic
    +
    filter.monomorphic

    (optional, logical) Default: filter.monomorphic = TRUE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -138,9 +140,7 @@

    Arguments

    Value

    - - -

    A list with the filtered input, whitelist and blacklist of markers..

    +

    A list with the filtered input, whitelist and blacklist of markers..

    See also

    @@ -155,10 +155,10 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 require(SeqArray) # when using gds
 mono <- radiator::filter_monomorphic(data = "my.radiator.gds.rad", verbose = TRUE)
-}
+} # }
    @@ -173,15 +173,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_rad.html b/docs/reference/filter_rad.html index 12726db3..79037f3f 100644 --- a/docs/reference/filter_rad.html +++ b/docs/reference/filter_rad.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -92,7 +92,9 @@

    ONE FUNCTION TO RULE THEM ALL

    Arguments

    -
    data
    + + +
    data

    14 options for input (diploid data only): VCFs (SNPs or Haplotypes, to make the vcf population ready), plink (tped, bed), stacks haplotype file, genind (library(adegenet)), @@ -108,7 +110,7 @@

    Arguments

    to understand it's limit before asking raditor to convert or filter your dataset.

    -
    strata
    +
    strata

    (optional) The strata file is a tab delimited file with a minimum of 2 columns headers: INDIVIDUALS and STRATA. Documented in read_strata. @@ -118,14 +120,14 @@

    Arguments

    Default: strata = NULL.

    -
    interactive.filter
    +
    interactive.filter

    (optional, logical) Do you want the filtering session to be interactive. Figures of distribution are shown before asking for filtering thresholds. Default: interactive.filter = TRUE.

    -
    output
    +
    output

    29 genomic data formats can be exported: tidy (by default), genepop, genind, genlight, vcf (for file format version, see details below), plink, structure, faststructure, arlequin, hierfstat, gtypes (strataG), @@ -141,40 +143,38 @@

    Arguments

    Default: output = NULL.

    -
    filename
    +
    filename

    (optional) The filename prefix for the objet in the global environment or the working directory. Default: filename = NULL. A default name will be used, customized with the output file(s) selected.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    ...
    +
    ...

    (optional) To pass further argument for fine-tuning the function.

    Value

    - - -

    The function returns an object (list). The content of the object +

    The function returns an object (list). The content of the object can be listed with names(object) and use $ to isolate specific object (see examples). Some output format will write the output file in the working directory. The tidy genomic data frame is generated automatically.

    Filtering steps and folders generated

    - +

    1. radiator:

      • the GDS file ending with .gds.rad. To open in R use read_rad.

      • filters_parameters.tsv: file containing all the parameters and @@ -359,7 +359,7 @@

        Filtering steps and folders generated

    Advance mode

    - +

    Ideally, use the function in interactive mode and forget about this section. @@ -402,7 +402,7 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # Some of the packages used in this function are not installed by default.
 # Installed the required packages:
 radiator_pkg_install()
@@ -419,7 +419,7 @@ 
    Examples
    
     strata = "strata.shark.tsv",
     output = "genind",
     filename = "shark")
-}
+} # }
    @@ -434,15 +434,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_snp_number.html b/docs/reference/filter_snp_number.html index 175f1517..13c6d77c 100644 --- a/docs/reference/filter_snp_number.html +++ b/docs/reference/filter_snp_number.html @@ -11,7 +11,7 @@ - +
    @@ -42,7 +42,7 @@
    • - +
    @@ -102,7 +102,9 @@

    Filter SNP number per locus/read

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -111,45 +113,45 @@

    Arguments

    tidy_vcf.

    -
    strata
    +
    strata

    (path or object) The strata file or object. Additional documentation is available in read_strata. Use that function to whitelist/blacklist populations/individuals. Option to set pop.levels/pop.labels is also available.

    -
    interactive.filter
    +
    interactive.filter

    (optional, logical) Do you want the filtering session to be interactive. Figures of distribution are shown before asking for filtering thresholds. Default: interactive.filter = TRUE.

    -
    filter.snp.number
    +
    filter.snp.number

    (integer) This is best decided after viewing the figures. If the argument is set to 2, locus with 3 and more SNPs will be blacklisted. Default: filter.snp.number = NULL.

    -
    filename
    +
    filename

    (optional) Name of the filtered tidy data frame file written to the working directory (ending with .tsv) Default: filename = NULL.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -157,9 +159,7 @@

    Arguments

    Value

    - - -

    A list in the global environment with 6 objects:

    1. $snp.number.markers

      2. +

      A list in the global environment with 6 objects:

      1. $snp.number.markers

      2. $number.snp.reads.plot

      3. $whitelist.markers

      4. $tidy.filtered.snp.number

        5. @@ -179,7 +179,7 @@

        Details

        Examples

        - 
        if (FALSE) {
+    
        if (FALSE) { # \dontrun{
 turtle.outlier.snp.number <- radiator::filter_snp_number(
 data = "turtle.vcf",
 strata = "turtle.strata.tsv",
@@ -192,7 +192,7 @@ 
        Examples
        
 #Inside the same list, to isolate the markers blacklisted:
 blacklist <- turtle.outlier.snp.number$blacklist.markers
 
-}
+} # }
        @@ -207,15 +207,15 @@

        Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_snp_position_read.html b/docs/reference/filter_snp_position_read.html index f748cf14..0a799860 100644 --- a/docs/reference/filter_snp_position_read.html +++ b/docs/reference/filter_snp_position_read.html @@ -9,7 +9,7 @@ - +
    @@ -40,7 +40,7 @@
    • - +
    @@ -98,7 +98,9 @@

    Filter markers/SNP based on their position on the read

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -107,21 +109,21 @@

    Arguments

    tidy_vcf.

    -
    strata
    +
    strata

    (path or object) The strata file or object. Additional documentation is available in read_strata. Use that function to whitelist/blacklist populations/individuals. Option to set pop.levels/pop.labels is also available.

    -
    interactive.filter
    +
    interactive.filter

    (optional, logical) Do you want the filtering session to be interactive. Figures of distribution are shown before asking for filtering thresholds. Default: interactive.filter = TRUE.

    -
    filter.snp.position.read
    +
    filter.snp.position.read

    (character) Options are: "outliers", "q75", "iqr", c(min value,max value). For a safe and conservative @@ -130,25 +132,25 @@

    Arguments

    Default: filter.snp.read.position = NULL.

    -
    filename
    +
    filename

    (optional) Name of the filtered tidy data frame file written to the working directory (ending with .tsv) Default: filename = NULL.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -156,9 +158,7 @@

    Arguments

    Value

    - - -

    A list in the global environment with 6 objects:

    1. $snp.number.markers

      2. +

      A list in the global environment with 6 objects:

      1. $snp.number.markers

      2. $number.snp.reads.plot

      3. $whitelist.markers

      4. $tidy.filtered.snp.number

        5. @@ -178,14 +178,14 @@

        Details

        Examples

        - 
        if (FALSE) {
+    
        if (FALSE) { # \dontrun{
 turtle <- radiator::filter_snp_position_read(
 data = "turtle.vcf",
 strata = "turtle.strata.tsv",
 filter.snp.position.read = "outliers",
 filename = "tidy.data.turtle.tsv"
 )
-}
+} # }
        @@ -200,15 +200,15 @@

        Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/filter_whitelist.html b/docs/reference/filter_whitelist.html index f7b87531..5a41ac24 100644 --- a/docs/reference/filter_whitelist.html +++ b/docs/reference/filter_whitelist.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -81,7 +81,9 @@

    Filter dataset with whitelist of markers

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -90,7 +92,7 @@

    Arguments

    tidy_vcf.

    -
    whitelist.markers
    +
    whitelist.markers

    (path or object) The whitelist is an object in your global environment or a file in the working directory (e.g. "whitelist.txt"). @@ -101,13 +103,13 @@

    Arguments

    Default whitelist.markers = NULL.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -124,9 +126,9 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 data <- radiator::filter_whitelist(data = data, whitelist.markers = "mywhitelist.tsv")
-}
+} # }
    @@ -141,15 +143,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/folder_prefix.html b/docs/reference/folder_prefix.html index 860196b6..fa870083 100644 --- a/docs/reference/folder_prefix.html +++ b/docs/reference/folder_prefix.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    folder_prefix

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/folder_short.html b/docs/reference/folder_short.html index 5e88a9f1..672d4ced 100644 --- a/docs/reference/folder_short.html +++ b/docs/reference/folder_short.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,7 +77,9 @@

    folder_short

    Arguments

    -
    f
    + + +
    f

    Folder name

    @@ -98,15 +100,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/gds2tidy.html b/docs/reference/gds2tidy.html index 406a219b..8c86877d 100644 --- a/docs/reference/gds2tidy.html +++ b/docs/reference/gds2tidy.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -100,15 +100,15 @@

    gds2tidy

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/generate_filename.html b/docs/reference/generate_filename.html index 1aa02089..6319f7dd 100644 --- a/docs/reference/generate_filename.html +++ b/docs/reference/generate_filename.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -95,15 +95,15 @@

    Filename radiator

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/generate_folder.html b/docs/reference/generate_folder.html index 7b999775..81b555e7 100644 --- a/docs/reference/generate_folder.html +++ b/docs/reference/generate_folder.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -85,34 +85,36 @@

    generate_folder

    Arguments

    -
    f
    + + +
    f

    Folder name

    -
    rad.folder
    +
    rad.folder

    Name of the rad folder

    -
    internal
    +
    internal

    (optional, logical) Is the function internal or not

    -
    append.date
    +
    append.date

    Include the date and time with the folder. Default: append.date = TRUE.

    -
    file.date
    +
    file.date

    The file date included in as argument/value or with default file.date = NULL, generated by the fucntion.

    -
    prefix_int
    +
    prefix_int

    Use an integer prefix padded left with 0. Default: prefix_int = TRUE.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -135,15 +137,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/generate_geno_freq_boundaries.html b/docs/reference/generate_geno_freq_boundaries.html index f1f93dac..190b8e9d 100644 --- a/docs/reference/generate_geno_freq_boundaries.html +++ b/docs/reference/generate_geno_freq_boundaries.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -98,15 +98,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/generate_hzar.html b/docs/reference/generate_hzar.html index 46736484..2be0fa9a 100644 --- a/docs/reference/generate_hzar.html +++ b/docs/reference/generate_hzar.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    generate_hzar

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/generate_markers_metadata.html b/docs/reference/generate_markers_metadata.html index cff386d9..c4140d35 100644 --- a/docs/reference/generate_markers_metadata.html +++ b/docs/reference/generate_markers_metadata.html @@ -4,7 +4,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -86,7 +86,9 @@

    Generate markers metadata

    Arguments

    -
    data
    + + +
    data

    An object with a column named MARKERS. If CHROM, LOCUS, POS are already present, the function returns the dataset untouched. @@ -94,14 +96,14 @@

    Arguments

    radiator GDS object.

    -
    generate.markers.metadata
    +
    generate.markers.metadata

    (logical, optional) Generate missing markers metadata when missing. "CHROM", "LOCUS", "POS". Default: generate.markers.metadata = TRUE

    -
    generate.ref.alt
    +
    generate.ref.alt

    (logical, optional) Generate missing REF/ALT alleles with: REF = A and ALT = C (for biallelic datasets, only). It is turned off automatically @@ -110,7 +112,7 @@

    Arguments

    Default: generate.ref.alt = FALSE

    -
    biallelic
    +
    biallelic

    (logical) Speed up the function execution by entering if the dataset is biallelic or not. Used internally for verification, before generating REF/ALT info. @@ -120,13 +122,13 @@

    Arguments

    Default: biallelic = NULL

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -134,9 +136,7 @@

    Arguments

    Value

    - - -

    Depending on argument's value, the same data is returned +

    Depending on argument's value, the same data is returned in the global environment, with potential these additional columns: CHROM, LOCUS, POS, REF, ALT.

    @@ -151,9 +151,9 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 tidy.data <- radiator::generate_markers_metadata(data = bluefintuna.data)
-}
+} # }
    @@ -168,15 +168,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/generate_squeleton_folders.html b/docs/reference/generate_squeleton_folders.html index 015475f9..9128a6d4 100644 --- a/docs/reference/generate_squeleton_folders.html +++ b/docs/reference/generate_squeleton_folders.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -93,15 +93,15 @@

    generate_squeleton_folders

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/generate_strata.html b/docs/reference/generate_strata.html index 38c59989..494a226e 100644 --- a/docs/reference/generate_strata.html +++ b/docs/reference/generate_strata.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -81,12 +81,14 @@

    Generate strata object from the data

    Arguments

    -
    data
    + + +
    data

    A tidy dataset object. Documented in tidy_genomic_data.

    -
    pop.id
    +
    pop.id

    (logical) When pop.id = TRUE, the strata returns the stratification colname POP_ID. Default: pop.id = FALSE, returns STRATA.

    @@ -115,15 +117,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/generate_whitelist.html b/docs/reference/generate_whitelist.html index bc9392d1..5257c3fa 100644 --- a/docs/reference/generate_whitelist.html +++ b/docs/reference/generate_whitelist.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -92,15 +92,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/genome_similarity.html b/docs/reference/genome_similarity.html index 866bbe25..082f7ee5 100644 --- a/docs/reference/genome_similarity.html +++ b/docs/reference/genome_similarity.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -95,15 +95,15 @@

    genome_similarity

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/genomic_converter.html b/docs/reference/genomic_converter.html index 2c671c2b..42ee7ca4 100644 --- a/docs/reference/genomic_converter.html +++ b/docs/reference/genomic_converter.html @@ -17,7 +17,7 @@ - +
    @@ -48,7 +48,7 @@
    • - +
    @@ -110,7 +110,9 @@

    Conversion tool among several genomic formats

    Arguments

    -
    data
    + + +
    data

    14 options for input (diploid data only): VCFs (SNPs or Haplotypes, to make the vcf population ready), plink (tped, bed), stacks haplotype file, genind (library(adegenet)), @@ -126,7 +128,7 @@

    Arguments

    to understand it's limit before asking raditor to convert or filter your dataset.

    -
    strata
    +
    strata

    (optional) The strata file is a tab delimited file with a minimum of 2 columns headers: INDIVIDUALS and STRATA. Documented in read_strata. @@ -136,7 +138,7 @@

    Arguments

    Default: strata = NULL.

    -
    output
    +
    output

    29 genomic data formats can be exported: tidy (by default), genepop, genind, genlight, vcf (for file format version, see details below), plink, structure, faststructure, arlequin, hierfstat, gtypes (strataG), @@ -152,40 +154,38 @@

    Arguments

    Default: output = NULL.

    -
    filename
    +
    filename

    (optional) The filename prefix for the object in the global environment or the working directory. Default: filename = NULL. A default name will be used, customized with the output file(s) selected.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) To pass further arguments for fine-tuning the function.

    Value

    - - -

    The function returns an object (list). The content of the object +

    The function returns an object (list). The content of the object can be listed with names(object) and use $ to isolate specific object (see examples). Some output format will write the output file in the working directory. The tidy genomic data frame is generated automatically.

    Input genomic datasets

    - +

    1. GDS file or object, must end with .gds or .rad: documented in read_vcf

      2. @@ -210,7 +210,7 @@

      Input genomic datasets

    Advance mode

    - +

    dots-dots-dots ... allows to pass several arguments for fine-tuning the function:

    1. path.folder: use this argument to specify an output folder. @@ -241,7 +241,7 @@

      Advance mode

    Life cycle

    - +

    Map-independent imputation of missing genotype is avaible in my other R @@ -262,7 +262,7 @@

    Life cycle

    VCF file format version

    - +

    If you need a different VCF file format version than the current one, just change @@ -330,7 +330,7 @@

    References

    Subpopulations (K) in Structured Populations. Genetics, 203, genetics.115.180992-1839.

    Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir BS, -Laurie C, Levine D (2017). SeqArray -- A storage-efficient high-performance +Laurie C, Levine D (2017). SeqArray – A storage-efficient high-performance data format for WGS variant calls. Bioinformatics.

    @@ -351,7 +351,7 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 #To verify your file is detected by radiator as the correct format:
 radiator::detect_genomic_format(data = "populations.snps.vcf")
 
@@ -365,7 +365,7 @@ 
    Examples
    
 names(snowcrab)
 #To isolate the genlight object (without imputation):
 genlight <- snowcrab$genlight
-}
+} # }
    @@ -380,15 +380,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/gt2array.html b/docs/reference/gt2array.html index 63c4beda..abe1f634 100644 --- a/docs/reference/gt2array.html +++ b/docs/reference/gt2array.html @@ -4,7 +4,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -90,15 +90,15 @@

    gt2array

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/haplotype_reconstruction.html b/docs/reference/haplotype_reconstruction.html index f5a412b2..eb664168 100644 --- a/docs/reference/haplotype_reconstruction.html +++ b/docs/reference/haplotype_reconstruction.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,7 +77,9 @@

    haplotype_reconstruction

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -86,7 +88,7 @@

    Arguments

    tidy_vcf.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    @@ -105,15 +107,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/hwe_analysis.html b/docs/reference/hwe_analysis.html index b6a96971..0c6dd082 100644 --- a/docs/reference/hwe_analysis.html +++ b/docs/reference/hwe_analysis.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -92,15 +92,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/ibdg_fh.html b/docs/reference/ibdg_fh.html index 0ccf1a3e..dafdf670 100644 --- a/docs/reference/ibdg_fh.html +++ b/docs/reference/ibdg_fh.html @@ -34,7 +34,7 @@ - +
    @@ -65,7 +65,7 @@
    • - +
    @@ -136,7 +136,9 @@

    FH measure of IBDg

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -145,39 +147,35 @@

    Arguments

    tidy_vcf.

    -
    path.folder
    +
    path.folder

    (path, optional) By default will print results in the working directory. Default: path.folder = NULL.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) To pass further arguments for fine-tuning the function.

    Value

    - - -

    A list is created with 4 objects:

    • $fh: the individual's FH values

      • +

      A list is created with 4 objects:

      • $fh: the individual's FH values

      • $fh.stats: the population and overall FH values. These values are calculated by averaging individual FH across samples and populations.

      • $fh.box.plot: the boxplot.

      • $fh.distribution.plot: the histogram.

      FH measure is on average negative when the parents are less related than -expected by random mating. The distribution fh.distribution.plot

      - - -

      should be centered around 0 in samples of non-inbred individuals.

      +expected by random mating. The distribution fh.distribution.plot +should be centered around 0 in samples of non-inbred individuals.

    Theory

    - +

    Modified FH: @@ -190,7 +188,7 @@

    Theory

    Advance mode

    - +

    dots-dots-dots ... allows to pass several arguments for fine-tuning the function. @@ -218,7 +216,7 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # Using a  VCF file, the simplest for of the function:
 fh <- ibdg_fh(data = "sturgeon.gds")
 
@@ -230,7 +228,7 @@ 
    Examples
    
 
 # To view the distribution of FH values:
 fh$fh.distribution.plot
-}
+} # }
    @@ -245,15 +243,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/import_dart.html b/docs/reference/import_dart.html index 17148602..06836213 100644 --- a/docs/reference/import_dart.html +++ b/docs/reference/import_dart.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -95,15 +95,15 @@

    import_dart

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/ind_total_reads.html b/docs/reference/ind_total_reads.html index 48a77ab6..3a2d24d7 100644 --- a/docs/reference/ind_total_reads.html +++ b/docs/reference/ind_total_reads.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    ind_total_reads

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 70645831..beb3936a 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,9 +1,9 @@ -Function reference • radiatorPackage index • radiator - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -570,15 +570,15 @@

    Run software
    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/individuals2strata.html b/docs/reference/individuals2strata.html index 3bc19983..ae0cc8f5 100644 --- a/docs/reference/individuals2strata.html +++ b/docs/reference/individuals2strata.html @@ -11,7 +11,7 @@ - +
    @@ -42,7 +42,7 @@
    • - +
    @@ -93,20 +93,22 @@

    Create a strata file from a list of individuals

    Arguments

    -
    data
    + + +
    data

    A file or data frame object with individuals in a column. The column name is INDIVIDUALS.

    -
    strata.start
    +
    strata.start

    (integer) The start of your strata id. See details for more info.

    -
    strata.end
    +
    strata.end

    (integer) The end of your strata id. See details for more info.

    -
    filename
    +
    filename

    (optional) The file name for the strata object if you want to save it in the working directory. Default: filename = NULL, the starta object is in the global @@ -115,9 +117,7 @@

    Arguments

    Value

    - - -

    a strata object and file, if requested. The file is tab delimited +

    a strata object and file, if requested. The file is tab delimited with 2 columns named: INDIVIDUALS and STRATA. The STRATA column can be any hierarchical grouping.

    @@ -146,14 +146,14 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 strata.abalone <- individuals2strata(
 data = "individuals.abalone.tsv",
 strata.start = 5,
 strata.end = 7,
 filename = "strata.abalone.tsv"
 )
-}
+} # }
    @@ -168,15 +168,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/join_strata.html b/docs/reference/join_strata.html index 9de248a4..7cffaa00 100644 --- a/docs/reference/join_strata.html +++ b/docs/reference/join_strata.html @@ -4,7 +4,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -79,25 +79,27 @@

    Join the strata with the data

    Arguments

    -
    data
    + + +
    data

    A tidy dataset object. Documented in tidy_genomic_data.

    -
    strata
    +
    strata

    (path or object) The strata file or object. Additional documentation is available in read_strata. Use that function to whitelist/blacklist populations/individuals. Option to set pop.levels/pop.labels is also available.

    -
    pop.id
    +
    pop.id

    (logical) When pop.id = TRUE, the strata returns the stratification colname POP_ID. Default: pop.id = FALSE, returns STRATA.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -105,9 +107,7 @@

    Arguments

    Value

    - - -

    The data filtered by the strata by individuals.

    +

    The data filtered by the strata by individuals.

    See also

    @@ -122,11 +122,11 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 data <- radiator::join_strata(
     data = my_tidy_dataset_object,
     strata = my_strata_object)
-}
+} # }
    @@ -141,15 +141,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/ld2df.html b/docs/reference/ld2df.html index 44ecc60a..787a5ead 100644 --- a/docs/reference/ld2df.html +++ b/docs/reference/ld2df.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    ld2df

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/ld_boxplot.html b/docs/reference/ld_boxplot.html index 08172eac..525aaa6c 100644 --- a/docs/reference/ld_boxplot.html +++ b/docs/reference/ld_boxplot.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -99,15 +99,15 @@

    ld_boxplot

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/ld_missing.html b/docs/reference/ld_missing.html index 281c0539..1d318418 100644 --- a/docs/reference/ld_missing.html +++ b/docs/reference/ld_missing.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -91,47 +91,47 @@

    Prune dataset based on LD and missingness.

    Arguments

    -
    wl
    + + +
    wl

    The split dataset by chromosome.

    -
    data
    +
    data

    The GDS object.

    -
    ld.threshold
    +
    ld.threshold

    The LD threshold.

    -
    denovo
    +
    denovo

    de novo data or not ? (logical).

    -
    ld.method
    +
    ld.method

    The method to compute LD.

    -
    ld.figures
    +
    ld.figures

    (logical, optional) Default: ld.figures = TRUE.

    -
    path.folder
    +
    path.folder

    (character) The path to the folder.

    -
    parallel.core
    +
    parallel.core

    The number of CPU.

    -
    verbose
    +
    verbose

    (logical, optional) Default: verbose = TRUE.

    Value

    - - -

    A list with whitelists and blacklists of markers in LD.

    +

    A list with whitelists and blacklists of markers in LD.

    Author

    @@ -150,15 +150,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/ld_pruning.html b/docs/reference/ld_pruning.html index a06bfd52..6ec1b5dc 100644 --- a/docs/reference/ld_pruning.html +++ b/docs/reference/ld_pruning.html @@ -4,7 +4,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -79,30 +79,30 @@

    Prune dataset based on LD.

    Arguments

    -
    ld.tibble
    + + +
    ld.tibble

    (path) The markers LD pairwise data. Default: ld.tibble = NULL.

    -
    stats
    +
    stats

    (path) The markers missingness info statistics. Default: stats = NULL.

    -
    ld.threshold
    +
    ld.threshold

    (double) The threshold to prune SNPs in LD. Default: ld.threshold = 0.8.

    -
    verbose
    +
    verbose

    (logical, optional) Default: verbose = TRUE.

    Value

    - - -

    A list with blacklisted SNPs. Write the blacklist in the working +

    A list with blacklisted SNPs. Write the blacklist in the working directory.

    @@ -122,15 +122,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/list_filters.html b/docs/reference/list_filters.html index 5ca12fc1..89711e9b 100644 --- a/docs/reference/list_filters.html +++ b/docs/reference/list_filters.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,7 +77,9 @@

    List current active filters (individuals and markers) in radiator GDS object

    Arguments

    -
    gds
    + + +
    gds

    (2 options) A Genomic Data Structure (GDS) file or object

    How to get GDS ? Look into tidy_genomic_data, @@ -96,10 +98,10 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # List active filters for individuals and markers
 list_filters(gds)
-}
+} # }
    @@ -114,15 +116,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/markers_genotyped_helper.html b/docs/reference/markers_genotyped_helper.html index cd407929..d56c60e0 100644 --- a/docs/reference/markers_genotyped_helper.html +++ b/docs/reference/markers_genotyped_helper.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    markers_genotyped_helper

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/merge_dart.html b/docs/reference/merge_dart.html index 8723034d..2a98ae61 100644 --- a/docs/reference/merge_dart.html +++ b/docs/reference/merge_dart.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,33 +88,35 @@

    Merge DArT files

    Arguments

    -
    dart1
    + + +
    dart1

    Full path of the first DArT file.

    -
    strata1
    +
    strata1

    Full path of the first strata file for dart1.

    -
    dart2
    +
    dart2

    Full path of the second DArT file.

    -
    strata2
    +
    strata2

    Full path of the second strata file for dart2.

    -
    filter.monomorphic
    +
    filter.monomorphic

    (optional, logical) Default: filter.monomorphic = TRUE.

    -
    filter.common.markers
    +
    filter.common.markers

    (optional, logical) Default: filter.common.markers = TRUE.

    -
    filename
    +
    filename

    Name of the merged DArT file. By default, the function gives the merged data the filename:merge_dart with date and time appended. The function will also append the date and time @@ -123,28 +125,26 @@

    Arguments

    Default: filename = NULL.

    -
    remove.non.immortalized.dart.markers
    +
    remove.non.immortalized.dart.markers

    (logical). By default the function will remove markers starting 1000, those are called non-immortalized markers by DArT. Default: remove.non.immortalized.dart.markers = TRUE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    ...
    +
    ...

    (optional) To pass further arguments for fine-tuning the function.

    Value

    - - -

    The function returns a list in the global environment and 2 data frames +

    The function returns a list in the global environment and 2 data frames in the working directory. The dataframes are the tidy dataset and a strata file of the 2 merged DArT files.

    @@ -172,12 +172,12 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # The simplest way to run the function:
 merged.data <- radiator::merge_dart(
 dart1 = "bluefin_larvae.tsv", strata1 = "strata1_bft_larvae.tsv",
 dart2 = "bluefin_adults.csv", strata2 = "strata2_bft_adults.tsv")
-}
+} # }
    @@ -192,15 +192,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/message_func_call.html b/docs/reference/message_func_call.html index eaaca50c..57ce0a7f 100644 --- a/docs/reference/message_func_call.html +++ b/docs/reference/message_func_call.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    message_func_call

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/missing_per_pop.html b/docs/reference/missing_per_pop.html index 1346923f..fae3c5e1 100644 --- a/docs/reference/missing_per_pop.html +++ b/docs/reference/missing_per_pop.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    missing_per_pop

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/n.html b/docs/reference/n.html index 5b50b0f3..5345c3be 100644 --- a/docs/reference/n.html +++ b/docs/reference/n.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    The number of observations in the current group.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/not_common_markers.html b/docs/reference/not_common_markers.html index 6ba27e6d..2c16a894 100644 --- a/docs/reference/not_common_markers.html +++ b/docs/reference/not_common_markers.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    not_common_markers

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/parallel_core_opt.html b/docs/reference/parallel_core_opt.html index f47a74b4..a4c337a3 100644 --- a/docs/reference/parallel_core_opt.html +++ b/docs/reference/parallel_core_opt.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    parallel_core_opt

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/parse_gds_metadata.html b/docs/reference/parse_gds_metadata.html index 5adb957c..1ade38e3 100644 --- a/docs/reference/parse_gds_metadata.html +++ b/docs/reference/parse_gds_metadata.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    parse_gds_metadata

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/pi.html b/docs/reference/pi.html index dca393ca..35510328 100644 --- a/docs/reference/pi.html +++ b/docs/reference/pi.html @@ -12,7 +12,7 @@ - +
    @@ -43,7 +43,7 @@
    • - +
    @@ -101,7 +101,9 @@

    Nucleotide diversity

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -110,24 +112,24 @@

    Arguments

    tidy_vcf.

    -
    read.length
    +
    read.length

    (integer, optional) The length in nucleotide of your reads. By default it is estimated from the data using the column COL. Default: read.length = NULL.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    path.folder
    +
    path.folder

    (path, optional) By default will print results in the working directory. Default: path.folder = NULL.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -135,9 +137,7 @@

    Arguments

    Value

    - - -

    The function returns a list with the function call and:

    1. $pi.individuals: the pi estimated for each individual

      2. +

      The function returns a list with the function call and:

      1. $pi.individuals: the pi estimated for each individual

      2. $pi.populations: the pi statistics estimated per populations and overall.

      3. $boxplot.pi: showing the boxplot of Pi for each populations and overall.

      use $ to access each #' objects in the list.

      @@ -162,11 +162,11 @@

      Author

      Examples

      - 
      if (FALSE) {
+    
      if (FALSE) { # \dontrun{
 require(stringdist)
 # The simplest way to run the function:
 pi.sum <- radiator::pi(data = "brook.charr.gds")
-}
+} # }
      @@ -181,15 +181,15 @@

      Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/pi_pop.html b/docs/reference/pi_pop.html index bf51afa8..ee19376a 100644 --- a/docs/reference/pi_pop.html +++ b/docs/reference/pi_pop.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -92,15 +92,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/pi_rad.html b/docs/reference/pi_rad.html index 01e38d49..ab6e86ba 100644 --- a/docs/reference/pi_rad.html +++ b/docs/reference/pi_rad.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -92,15 +92,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/pipe.html b/docs/reference/pipe.html index f9deeb3f..5f7effed 100644 --- a/docs/reference/pipe.html +++ b/docs/reference/pipe.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    Forward-pipe operator

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plot_bayescan.html b/docs/reference/plot_bayescan.html index 9b825746..ac13edd3 100644 --- a/docs/reference/plot_bayescan.html +++ b/docs/reference/plot_bayescan.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    plot_bayescan

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plot_boxplot_coverage.html b/docs/reference/plot_boxplot_coverage.html index 96c2c302..1119337b 100644 --- a/docs/reference/plot_boxplot_coverage.html +++ b/docs/reference/plot_boxplot_coverage.html @@ -4,7 +4,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -79,7 +79,9 @@

    Figure box plot of coverage summary statistics

    Arguments

    -
    data
    + + +
    data

    Coverage summary file.

    @@ -96,15 +98,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plot_boxplot_diversity.html b/docs/reference/plot_boxplot_diversity.html index 37465750..18e4f962 100644 --- a/docs/reference/plot_boxplot_diversity.html +++ b/docs/reference/plot_boxplot_diversity.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -91,38 +91,40 @@

    Box plot of the diversity (Gene and Haplotypes)

    Arguments

    -
    data
    + + +
    data

    containing the stats

    -
    aes.x.y
    +
    aes.x.y

    The GGPLOT2 aesthetics, e.g. aes.x.y = aes(x = factor(POP_ID), y = GENE_DIVERSITY, na.rm = T).

    -
    y.title
    +
    y.title

    Title of the y-axis.

    -
    strata
    +
    strata

    Containing strata info for the visual. Default: strata = FALSE.

    -
    stats
    +
    stats

    e.g. MAC, MAF or MAD.

    -
    x.axis.title
    +
    x.axis.title

    Title for the x axis

    -
    text.orientation
    +
    text.orientation

    Orientation of the x axis text. Default: text.orientation = "horizontal"horizontal.

    -
    plot.filename
    +
    plot.filename

    To save the figure provide a filename. Default: plot.filename = NULL

    @@ -140,15 +142,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plot_coverage_imbalance_diagnostic.html b/docs/reference/plot_coverage_imbalance_diagnostic.html index dbf6299f..a8d99ac3 100644 --- a/docs/reference/plot_coverage_imbalance_diagnostic.html +++ b/docs/reference/plot_coverage_imbalance_diagnostic.html @@ -7,7 +7,7 @@ - +
    @@ -38,7 +38,7 @@
    • - +
    @@ -91,32 +91,32 @@

    Visual diagnostic of coverage imbalance

    Arguments

    -
    tidy.vcf.file
    + + +
    tidy.vcf.file

    The tidy VCF file created with tidy_genomic_data.

    -
    pop.levels
    +
    pop.levels

    Character string defining your ordered populations.

    -
    read.depth.threshold
    +
    read.depth.threshold

    Define the threshold you wish to analyse.

    -
    aes.colour
    +
    aes.colour

    GGPLOT2 aesthetics, e.g. aes(y = ..count..).

    -
    adjust.bin
    +
    adjust.bin

    Adjust GGPLOT2 bin size (0 to 1).

    Value

    - - -

    4-plots highlighting the different combination of under +

    4-plots highlighting the different combination of under or over the coverage threshold and mean genotype likelihood. Y- axis show the distribution of genotypes. X- axis show the coverage imbalance the @@ -149,15 +149,15 @@

    Details

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plot_density_distribution_coverage.html b/docs/reference/plot_density_distribution_coverage.html index 53d862f6..e00ec3c4 100644 --- a/docs/reference/plot_density_distribution_coverage.html +++ b/docs/reference/plot_density_distribution_coverage.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -85,16 +85,18 @@

    Figure of distribution (histogram)

    Arguments

    -
    data
    + + +
    data

    Coverage summary file.

    -
    aes.colour
    +
    aes.colour

    GGPLOT2 aesthetics colour, e.g. aes(y = ..scaled.., color = COVERAGE_GROUP).

    -
    adjust.bin
    +
    adjust.bin

    Adjust GGPLOT2 bin size (0 to 1).

    @@ -111,15 +113,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plot_density_distribution_het.html b/docs/reference/plot_density_distribution_het.html index 428ecc0c..e6a9575b 100644 --- a/docs/reference/plot_density_distribution_het.html +++ b/docs/reference/plot_density_distribution_het.html @@ -4,7 +4,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -86,28 +86,30 @@

    Figure density distribution of the observed heterozygosity summary statistic

    Arguments

    -
    data
    + + +
    data

    sumstats or tidy vcf files.

    -
    pop.levels
    +
    pop.levels

    Character string defining your ordered populations.

    -
    het.group
    +
    het.group

    = aes(x = HET_MAX, na.rm = F)

    -
    aes.colour
    +
    aes.colour

    GGPLOT2 aesthetics colour, e.g. aes(y = ..scaled.., color = GROUP).

    -
    adjust.bin
    +
    adjust.bin

    Adjust GGPLOT2 bin size (0 to 1).

    -
    x.title
    +
    x.title

    Title of the x-axis.

    @@ -124,15 +126,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plot_density_distribution_maf.html b/docs/reference/plot_density_distribution_maf.html index 666d57e1..98d15bc4 100644 --- a/docs/reference/plot_density_distribution_maf.html +++ b/docs/reference/plot_density_distribution_maf.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -83,24 +83,26 @@

    Figure density distribution of minor allele frequency (MAF) summary statisti

    Arguments

    -
    data
    + + +
    data

    sumstats or tidy vcf summarised files.

    -
    maf.group
    +
    maf.group

    The GGPLOT2 aes (e.g. aes(x = FREQ_ALT, na.rm = F)).

    -
    aes.colour
    +
    aes.colour

    GGPLOT2 aesthetics colour, e.g. aes(y = ..scaled.., color = POP_ID) or aes(y = ..count.., color = POP_ID)

    -
    adjust.bin
    +
    adjust.bin

    Adjust GGPLOT2 bin size (0 to 1).

    -
    x.title
    +
    x.title

    Title of the x-axis. e.g. "MAF distribution"

    @@ -131,15 +133,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plot_distribution_diversity.html b/docs/reference/plot_distribution_diversity.html index 7790f744..0948c2d7 100644 --- a/docs/reference/plot_distribution_diversity.html +++ b/docs/reference/plot_distribution_diversity.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,25 +77,27 @@

    Density distribution of diversity (Gene and Haplotypes)

    Arguments

    -
    data
    + + +
    data

    The hapstats summary file or object.

    -
    aes.x
    +
    aes.x

    GGPLOT2 aesthetics, e.g. aes.x = aes(x = GENE_DIVERSITY, na.rm = T).

    -
    aes.colour
    +
    aes.colour

    GGPLOT2 aesthetics colour, e.g. aes.colour = aes(y = ..scaled.., colour = POP_ID).

    -
    x.title
    +
    x.title

    Title of the x-axis.

    -
    y.title
    +
    y.title

    Title of the y-axis.

    @@ -112,15 +114,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plot_het_outliers.html b/docs/reference/plot_het_outliers.html index a108a532..c35a0b98 100644 --- a/docs/reference/plot_het_outliers.html +++ b/docs/reference/plot_het_outliers.html @@ -4,7 +4,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -95,15 +95,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plot_snp_number_loci.html b/docs/reference/plot_snp_number_loci.html index 9ce9a822..77be1b2f 100644 --- a/docs/reference/plot_snp_number_loci.html +++ b/docs/reference/plot_snp_number_loci.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,11 +77,13 @@

    Figure of the distribution of SNP per locus before and after filters

    Arguments

    -
    before.filter.data
    + + +
    before.filter.data

    Data set before filter.

    -
    after.filter.data
    +
    after.filter.data

    Data set after filter.

    @@ -98,15 +100,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plot_snp_position_read.html b/docs/reference/plot_snp_position_read.html index 2dcbf6dd..7ea0c3f6 100644 --- a/docs/reference/plot_snp_position_read.html +++ b/docs/reference/plot_snp_position_read.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,15 +77,17 @@

    Figure of the distribution of SNP nucleotide position alond the read

    Arguments

    -
    data
    + + +
    data

    Data for the figure.

    -
    aes.colour
    +
    aes.colour

    GGPLOT2 aesthetic.

    -
    y.title
    +
    y.title

    Title of the Y-axis.

    @@ -102,15 +104,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plot_upset.html b/docs/reference/plot_upset.html index cb52c6bc..1ccb58af 100644 --- a/docs/reference/plot_upset.html +++ b/docs/reference/plot_upset.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -94,15 +94,15 @@

    plot_upset

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/private_alleles.html b/docs/reference/private_alleles.html index ec6b6f9f..5df89740 100644 --- a/docs/reference/private_alleles.html +++ b/docs/reference/private_alleles.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,7 +77,9 @@

    Find private alleles

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -86,14 +88,14 @@

    Arguments

    tidy_vcf.

    -
    strata
    +
    strata

    (path or object) The strata file or object. Additional documentation is available in read_strata. Use that function to whitelist/blacklist populations/individuals. Option to set pop.levels/pop.labels is also available.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -101,9 +103,7 @@

    Arguments

    Value

    - - -

    A list with an object highlighting private alleles by markers and strata and +

    A list with an object highlighting private alleles by markers and strata and a second object with private alleles summarized by strata.

    @@ -113,9 +113,9 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 corals.private.alleles.by.pop <- radiator::private_alleles(data = tidy, strata = strata.pop)
-}
+} # }
    @@ -130,15 +130,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/private_haplotypes.html b/docs/reference/private_haplotypes.html index 7c2c60ea..06fbb519 100644 --- a/docs/reference/private_haplotypes.html +++ b/docs/reference/private_haplotypes.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,7 +77,9 @@

    private haplotypes

    Arguments

    -
    data
    + + +
    data

    A tidy genomic dataframe Used internally in radiator and might be of interest for users. @@ -85,7 +87,7 @@

    Arguments

    Look into radiator tidy_genomic_data.

    -
    strata
    +
    strata

    (optional) A strata file or object in the global environment. The strata is a tab-separated data frame with 2 columns: INDIVIDUALS and STRATA. If used, the strata will replace the current STRATA or POP_ID in the @@ -93,7 +95,7 @@

    Arguments

    hierarchical level, other than POP_ID.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -101,9 +103,7 @@

    Arguments

    Value

    - - -

    A list with private haplotypes per markers and strata and a summary of +

    A list with private haplotypes per markers and strata and a summary of overall number of private haplotypes per strata.

    @@ -123,15 +123,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_common_arguments.html b/docs/reference/radiator_common_arguments.html index 60ef0e9e..0638b378 100644 --- a/docs/reference/radiator_common_arguments.html +++ b/docs/reference/radiator_common_arguments.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -85,14 +85,16 @@

    radiator common arguments

    Arguments

    -
    interactive.filter
    + + +
    interactive.filter

    (optional, logical) Do you want the filtering session to be interactive. Figures of distribution are shown before asking for filtering thresholds. Default: interactive.filter = TRUE.

    -
    gds
    +
    gds

    (2 options) A Genomic Data Structure (GDS) file or object

    How to get GDS ? Look into tidy_genomic_data, @@ -100,7 +102,7 @@

    Arguments

    tidy_vcf or write_gds.

    -
    data
    +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -109,26 +111,26 @@

    Arguments

    tidy_vcf.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    random.seed
    +
    random.seed

    (integer, optional) For reproducibility, set an integer that will be used inside the function that requires randomness. With default, a random number is generated and printed in the appropriate output. Default: random.seed = NULL.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -147,15 +149,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_dots.html b/docs/reference/radiator_dots.html index f469fad2..63cf5d42 100644 --- a/docs/reference/radiator_dots.html +++ b/docs/reference/radiator_dots.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -108,25 +108,27 @@

    radiator_dots

    Arguments

    -
    func.name
    + + +
    func.name

    Default: as.list(sys.call())[[1]].

    -
    fd
    +
    fd

    (optional) Default: rlang::fn_fmls_names().

    -
    args.list
    +
    args.list

    (optional) Default:args.list = as.list(environment()).

    -
    dotslist
    +
    dotslist

    The dots dots dots arguments captured. Default: dotslist = rlang::dots_list(..., .homonyms = "error", .check_assign = TRUE).

    -
    keepers
    +
    keepers

    (optional) The arguments that are used inside the function. Default: keepers = c( "subsample.markers.stats", "subsample", @@ -155,7 +157,7 @@

    Arguments

    "sex.id.input", "het.qr.input").

    -
    deprecated
    +
    deprecated

    (optional) radiator's deprecated arguments. Default: deprecated = c("maf.thresholds", "common.markers", "max.marker","monomorphic.out", "snp.ld", "filter.call.rate", @@ -163,7 +165,7 @@

    Arguments

    "mixed.genomes.analysis", "duplicate.genomes.analysis", "maf.data", "ref.calibration").

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -182,15 +184,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_folder.html b/docs/reference/radiator_folder.html index 56a8c2a9..ef48fc51 100644 --- a/docs/reference/radiator_folder.html +++ b/docs/reference/radiator_folder.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,15 +77,17 @@

    radiator_folder

    Arguments

    -
    f
    + + +
    f

    Folder name

    -
    path.folder
    +
    path.folder

    path of the folder

    -
    prefix_int
    +
    prefix_int

    Use an integer prefix padded left with 0. Default: prefix_int = TRUE.

    @@ -107,15 +109,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_function_header.html b/docs/reference/radiator_function_header.html index 4f2a84cd..6b1039c4 100644 --- a/docs/reference/radiator_function_header.html +++ b/docs/reference/radiator_function_header.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    radiator_function_header

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_gds.html b/docs/reference/radiator_gds.html index 71e90e1c..5c33f4f9 100644 --- a/docs/reference/radiator_gds.html +++ b/docs/reference/radiator_gds.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -102,15 +102,15 @@

    radiator gds constructor

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_gds_skeleton.html b/docs/reference/radiator_gds_skeleton.html index a6e87360..e86a5730 100644 --- a/docs/reference/radiator_gds_skeleton.html +++ b/docs/reference/radiator_gds_skeleton.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    radiator_gds_skeleton

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_packages_dep.html b/docs/reference/radiator_packages_dep.html index c09d106b..c0cf7a77 100644 --- a/docs/reference/radiator_packages_dep.html +++ b/docs/reference/radiator_packages_dep.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    radiator_packages_dep

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_parameters.html b/docs/reference/radiator_parameters.html index d346f70e..315365e3 100644 --- a/docs/reference/radiator_parameters.html +++ b/docs/reference/radiator_parameters.html @@ -4,7 +4,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -105,15 +105,15 @@

    radiator_parameters

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_pkg_install.html b/docs/reference/radiator_pkg_install.html index da4afa13..bd4ab285 100644 --- a/docs/reference/radiator_pkg_install.html +++ b/docs/reference/radiator_pkg_install.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -81,12 +81,14 @@

    radiator packages install helper

    Arguments

    -
    check
    + + +
    check

    (logical, optional) Check the packages installed and system info. Default: check = TRUE

    -
    minimal.install
    +
    minimal.install

    (logical, optional) The minimal install does nothing, and the function just check what's installed. Default: check = FALSE, does the full installation of packages you might @@ -106,15 +108,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_question.html b/docs/reference/radiator_question.html index 866811f5..c5819749 100644 --- a/docs/reference/radiator_question.html +++ b/docs/reference/radiator_question.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    radiator_question

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_results_message.html b/docs/reference/radiator_results_message.html index ac45dcd1..e52bd2c4 100644 --- a/docs/reference/radiator_results_message.html +++ b/docs/reference/radiator_results_message.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -93,15 +93,15 @@

    radiator_results_message

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_snakecase.html b/docs/reference/radiator_snakecase.html index a957cc7c..89fb1b32 100644 --- a/docs/reference/radiator_snakecase.html +++ b/docs/reference/radiator_snakecase.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    radiator_snakecase

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_split_tibble.html b/docs/reference/radiator_split_tibble.html index b94c3d77..5cd09c58 100644 --- a/docs/reference/radiator_split_tibble.html +++ b/docs/reference/radiator_split_tibble.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    radiator_split_tibble

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_tic.html b/docs/reference/radiator_tic.html index d5138c6e..f8ea1139 100644 --- a/docs/reference/radiator_tic.html +++ b/docs/reference/radiator_tic.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    radiator_tic

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/radiator_toc.html b/docs/reference/radiator_toc.html index 00d8bea4..469adb5a 100644 --- a/docs/reference/radiator_toc.html +++ b/docs/reference/radiator_toc.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -92,15 +92,15 @@

    radiator_toc

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/read_blacklist_genotypes.html b/docs/reference/read_blacklist_genotypes.html index 45c84543..869df6ef 100644 --- a/docs/reference/read_blacklist_genotypes.html +++ b/docs/reference/read_blacklist_genotypes.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,7 +83,9 @@

    read blacklist of genotypes

    Arguments

    -
    blacklist.genotypes
    + + +
    blacklist.genotypes

    (path or object) The blacklist is an object in your global environment or a file in the working directory (e.g. "blacklist.geno.tsv"). @@ -97,13 +99,13 @@

    Arguments

    Default blacklist.genotypes = NULL.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -111,7 +113,7 @@

    Arguments

    Life cycle

    - +

    This function arguments will be subject to changes. Currently the function uses @@ -126,10 +128,10 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 bl <- radiator::read_blacklist_genotypes(data = data,
     blacklist.genotypes = "blacklist.geno.iguana.tsv")
-}
+} # }
    @@ -144,15 +146,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/read_blacklist_id.html b/docs/reference/read_blacklist_id.html index 17bd0c87..2d723656 100644 --- a/docs/reference/read_blacklist_id.html +++ b/docs/reference/read_blacklist_id.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -81,7 +81,9 @@

    read_blacklist_id

    Arguments

    -
    blacklist.id
    + + +
    blacklist.id

    (optional, path or object) A blacklist file in the working directory or object in the global environment. The data frame as 1 column (named INDIVIDUALS) and is filled with the individual IDs @@ -90,7 +92,7 @@

    Arguments

    Default: blacklist.id = NULL.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -98,16 +100,14 @@

    Arguments

    Value

    - - -

    A tibble with column INDIVIDUALS.

    +

    A tibble with column INDIVIDUALS.

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 bl <- radiator::read_blacklist_id("blacklist.tsv")
-}
+} # }
    @@ -122,15 +122,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/read_dart.html b/docs/reference/read_dart.html index 460c42b6..844a9a5f 100644 --- a/docs/reference/read_dart.html +++ b/docs/reference/read_dart.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -91,7 +91,9 @@

    Read and tidy

    Arguments

    -
    data
    + + +
    data

    One of the DArT output files. 6 formats used by DArT are recognized by radiator. recognised:

    1. 1row: Genotypes are in 1 row and coded (0, 1, 2, -). @@ -116,7 +118,7 @@

      Arguments

      the function.

    -
    strata
    +
    strata

    A tab delimited file or object with 3 columns. Columns header is: TARGET_ID, INDIVIDUALS and STRATA. @@ -135,7 +137,7 @@

    Arguments

    example.dart.strata.tsv.

    -
    filename
    +
    filename

    (optional) The function uses write.fst, to write the tidy data frame in the working directory. The file extension appended to @@ -144,40 +146,34 @@

    Arguments

    in the global environment only (i.e. not written in the working directory...).

    -
    tidy.dart
    +
    tidy.dart

    (logical, optional) Generate a tidy dataset. Default:tidy.dart = FALSE.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    ...
    +
    ...

    (optional) To pass further argument for fine-tuning the function.

    Value

    - - -

    A radiator GDS file and tidy dataframe with several columns depending on DArT file: +

    A radiator GDS file and tidy dataframe with several columns depending on DArT file: silico.dart: A tibble with 5 columns: CLONE_ID, SEQUENCE, VALUE, INDIVIDUALS, STRATA. This object is also saved in the directory (file ending with .rad).

    - -

    Common to 1row, 2rows and counts: A GDS file is automatically generated. To have a tidy tibble, the argument tidy.dart = TRUE must be used.

    - -

    1. VARIANT_ID: generated by radiator and correspond the markers in integer.

    2. MARKERS: generated by radiator and correspond to CHROM + LOCUS + POS separated by 2 underscores.

    3. CHROM: the chromosome info, for de novo: CHROM_1.

      4. @@ -209,7 +205,7 @@

      Value

    Advance mode

    - +

    dots-dots-dots ... allows to pass several arguments for fine-tuning the function:

    1. whitelist.markers: detailed in filter_whitelist. @@ -235,12 +231,12 @@

      Author

      Examples

      - 
      if (FALSE) {
+    
      if (FALSE) { # \dontrun{
 clownfish.dart.tidy <- radiator::read_dart(
     data = "clownfish.dart.csv",
     strata = "clownfish.strata.tsv"
     )
-}
+} # }
      @@ -255,15 +251,15 @@

      Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/read_plink.html b/docs/reference/read_plink.html index 57fecb34..fea2e072 100644 --- a/docs/reference/read_plink.html +++ b/docs/reference/read_plink.html @@ -10,7 +10,7 @@ - +
    @@ -41,7 +41,7 @@
    • - +
    @@ -97,7 +97,9 @@

    Reads PLINK tped and bed files

    Arguments

    -
    data
    + + +
    data

    The PLINK file.

    • bi-allelic data only. For haplotypes use VCF.

    • tped file format: the corresponding tfam file must be in the directory.

    • bed file format: IS THE PREFERRED format, the corresponding @@ -105,7 +107,7 @@

      Arguments

    -
    filename
    +
    filename

    (optional) The file name of the Genomic Data Structure (GDS) file. radiator will append .gds.rad to the filename. If the filename chosen exists in the working directory, @@ -113,27 +115,25 @@

    Arguments

    Default: filename = NULL.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) To pass further arguments for fine-tuning the function.

    Value

    - - -

    For tped the function returns a list object with the non-modified tped and +

    For tped the function returns a list object with the non-modified tped and the strata corresponding to the tfam. With bed, the function returns a GDS object.

    @@ -148,7 +148,7 @@

    Details

    References

    Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir BS, -Laurie C, Levine D (2017). SeqArray -- A storage-efficient high-performance +Laurie C, Levine D (2017). SeqArray – A storage-efficient high-performance data format for WGS variant calls. Bioinformatics.

    PLINK: a tool set for whole-genome association and population-based linkage @@ -166,11 +166,11 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 data <- radiator::read_plink(data = "my_plink_file.bed")
 # when conversion is required from TPED to BED, in Terminal:
 # plink --tfile my_plink_file --make-bed --allow-no-sex --allow-extra-chr --chr-set 95
-}
+} # }
    @@ -185,15 +185,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/read_rad.html b/docs/reference/read_rad.html index 44c52659..697d354b 100644 --- a/docs/reference/read_rad.html +++ b/docs/reference/read_rad.html @@ -10,7 +10,7 @@ - +
    @@ -41,7 +41,7 @@
    • - +
    @@ -101,28 +101,30 @@

    Read radiator file ending .gds, .rad, .gds.rad.

    Arguments

    -
    data
    + + +
    data

    A file in the working directory ending with .rad or .gds, and produced by radiator, assigner or grur.

    -
    columns
    +
    columns

    (optional) For fst file. Column names to read. The default is to read all all columns. Default: columns = NULL.

    -
    from
    +
    from

    (optional) For fst file. Read data starting from this row number. Default: from = 1.

    -
    to
    +
    to

    (optional) For fst file. Read data up until this row number. The default is to read to the last row of the stored dataset. Default: to = NULL.

    -
    as.data.table
    +
    as.data.table

    (optional, logical) For fst file. If TRUE, the result will be returned as a data.table object. Any keys set on dataset x before writing will be retained. @@ -130,25 +132,25 @@

    Arguments

    Default: as.data.table = TRUE.

    -
    old.format
    +
    old.format

    (optional, logical) For fst file. Use TRUE to read fst files generated with a fst package version lower than v.0.8.0 Default: old.format = FALSE.

    -
    allow.dup
    +
    allow.dup

    (optional, logical) To allow the opening of a GDS file with read-only mode when it has been opened in the same R session. Default: allow.dup = FALSE.

    -
    check
    +
    check

    (optional, logical) Verify that GDS number of samples and markers match. Default: check = TRUE.

    -
    verbose
    +
    verbose

    (optional, logical) verbose = TRUE to be chatty during execution. Default: verbose = FALSE.

    @@ -156,9 +158,7 @@

    Arguments

    Value

    - - -

    A radiator tidy data frame or +

    A radiator tidy data frame or GDS object (with read/write permissions) in the global environment.

    @@ -179,11 +179,11 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 require(SeqArray)
 shark <- radiator::read_rad(data = "data.shark.gds")
 turtle <- radiator::read_rad(data = "data.turtle.rad")
-}
+} # }
    @@ -198,15 +198,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/read_strata.html b/docs/reference/read_strata.html index d9eb6450..7be1cbf5 100644 --- a/docs/reference/read_strata.html +++ b/docs/reference/read_strata.html @@ -7,7 +7,7 @@ - +
    @@ -38,7 +38,7 @@
    • - +
    @@ -96,20 +96,22 @@

    read strata

    Arguments

    -
    strata
    + + +
    strata

    (path or object) The strata file or object. Additional documentation is available in read_strata. Use that function to whitelist/blacklist populations/individuals. Option to set pop.levels/pop.labels is also available.

    -
    pop.id
    +
    pop.id

    (logical) When pop.id = TRUE, the strata returns the stratification colname POP_ID. Default: pop.id = FALSE, returns STRATA.

    -
    pop.levels
    +
    pop.levels

    (optional, string) This refers to the levels in a factor. In this case, the id of the pop. Use this argument to have the pop ordered your way instead of the default @@ -119,7 +121,7 @@

    Arguments

    Default: pop.levels = NULL.

    -
    pop.labels
    +
    pop.labels

    (optional, string) Use this argument to rename/relabel your pop or combine your pop. e.g. To combine "QUE" and "ONT" into a new pop called "NEW": @@ -135,14 +137,14 @@

    Arguments

    White spaces in population names are replaced by underscore.

    -
    pop.select
    +
    pop.select

    (optional, string) Selected list of populations for the analysis. e.g. pop.select = c("QUE", "ONT") to select QUE and ONT population samples (out of 20 pops). Default: pop.select = NULL

    -
    blacklist.id
    +
    blacklist.id

    (optional, path or object) A blacklist file in the working directory or object in the global environment. The data frame as 1 column (named INDIVIDUALS) and is filled with the individual IDs @@ -151,20 +153,20 @@

    Arguments

    Default: blacklist.id = NULL.

    -
    keep.two
    +
    keep.two

    (optional, logical) The output is limited to 2 columns: INDIVIDUALS, STRATA. Default: keep.two = TRUE.

    -
    path.folder
    +
    path.folder

    (optional, path) If !is.null(blacklist.id) || !is.null(pop.select), the modified strata is written by default in the working directory. Default: path.folder = getwd().

    -
    filename
    +
    filename

    (optional, character) If !is.null(blacklist.id) || !is.null(pop.select), the modified strata is written by default in the working directory with date and time appended to strata_radiator_filtered, @@ -173,7 +175,7 @@

    Arguments

    Default: filename = NULL.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -181,9 +183,7 @@

    Arguments

    Value

    - - -

    A list with several components:

    1. $strata

      2. +

      A list with several components:

      1. $strata

      2. $pop.levels

      3. $pop.labels

      4. $pop.select

        5. @@ -216,14 +216,14 @@

        Details

    VCF

    - +

    VCF file users, not sure about the sample id inside your file ? See the example in extract_individuals_vcf

    DArT

    - +

    DArT file users, not sure about the sample id inside your file ? See the example in extract_dart_target_id

    @@ -237,7 +237,7 @@

    See also

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 strata.info <- radiator::read_strata(strata)
 
 # the return object is a list with 5 objects:
@@ -254,7 +254,7 @@ 
    Examples
    
     blacklist.id = "blacklisted.ids.tsv"
     )
 
-}
+} # }
    @@ -269,15 +269,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/read_vcf.html b/docs/reference/read_vcf.html index 7e2e5c9c..a368b6b9 100644 --- a/docs/reference/read_vcf.html +++ b/docs/reference/read_vcf.html @@ -13,7 +13,7 @@ - +
    @@ -44,7 +44,7 @@
    • - +
    @@ -105,7 +105,9 @@

    Read VCF files and write a GDS file

    Arguments

    -
    data
    + + +
    data

    (path, character) The VCF markers are biallelic SNPs or haplotypes. To make the VCF population-ready, you have to use strata argument.

    • GATK, platypus, samtools and ipyrad VCFs: @@ -130,7 +132,7 @@

      Arguments

    -
    strata
    +
    strata

    (optional) The strata file is a tab delimited file with a minimum of 2 columns headers: INDIVIDUALS and STRATA. Documented in read_strata. @@ -140,7 +142,7 @@

    Arguments

    Default: strata = NULL.

    -
    filename
    +
    filename

    (optional) The file name of the Genomic Data Structure (GDS) file. radiator will append .gds.rad to the filename. If the filename chosen exists in the working directory, @@ -148,7 +150,7 @@

    Arguments

    Default: filename = NULL.

    -
    vcf.stats
    +
    vcf.stats

    (optional, logical) Generates individuals and markers statistics helpful for filtering. These are very fast to generate and because computational @@ -160,27 +162,25 @@

    Arguments

    Default: vcf.stats = TRUE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) To pass further arguments for fine-tuning the function.

    Value

    - - -

    The function returns a GDS object.

    +

    The function returns a GDS object.

    Details

    @@ -203,7 +203,7 @@

    Details

    VCF file format

    - +

    PLINK: radiator fills the LOCUS column of PLINK VCFs with @@ -236,7 +236,7 @@

    VCF file format

    Advance mode

    - +

    dots-dots-dots ... allows to pass several arguments for fine-tuning the function:

    1. whitelist.markers: detailed in filter_whitelist.

      2. @@ -310,7 +310,7 @@

      Advance mode

      References

      Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir BS, -Laurie C, Levine D (2017). SeqArray -- A storage-efficient high-performance +Laurie C, Levine D (2017). SeqArray – A storage-efficient high-performance data format for WGS variant calls. Bioinformatics.

      Danecek P, Auton A, Abecasis G et al. (2011) @@ -330,7 +330,7 @@

      Author

      Examples

      - 
      if (FALSE) {
+    
      if (FALSE) { # \dontrun{
 # require(SeqArray)
 # with built-in defaults:
 
@@ -361,7 +361,7 @@ 
      Examples
      
 # In a new R session, to re-open the GDS file/connection:
 
 data <- radiator::read_rad(data = "radiator_20200911@0748.gds")
-}
+} # }
      @@ -376,15 +376,15 @@

      Examples

      -

      Site built with pkgdown 2.0.9.

      +

      Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/read_whitelist.html b/docs/reference/read_whitelist.html index 284160d3..d5330b98 100644 --- a/docs/reference/read_whitelist.html +++ b/docs/reference/read_whitelist.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,7 +83,9 @@

    read whitelist of markers

    Arguments

    -
    whitelist.markers
    + + +
    whitelist.markers

    (path or object) The whitelist is an object in your global environment or a file in the working directory (e.g. "whitelist.txt"). @@ -94,7 +96,7 @@

    Arguments

    Default whitelist.markers = NULL.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -119,9 +121,9 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 wl <- radiator::read_whitelist(data = data, whitelist.markers = "mywhitelist.tsv")
-}
+} # }
    @@ -136,15 +138,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/remove_duplicates.html b/docs/reference/remove_duplicates.html index 24322e7d..b33f3632 100644 --- a/docs/reference/remove_duplicates.html +++ b/docs/reference/remove_duplicates.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -87,22 +87,24 @@

    Read tidy genomic data file ending .rad

    Arguments

    -
    data
    + + +
    data

    (path) The individual's pairwise data. Default: data = "individuals.pairwise.dist.tsv".

    -
    stats
    +
    stats

    (path) The genotype statistics Default: stats = "genotyped.statistics.tsv".

    -
    dup.threshold
    +
    dup.threshold

    (double) The threshold to filter out duplicates Default: dup.threshold = 0.25.

    -
    diff.pop.remove
    +
    diff.pop.remove

    Remove all individuals in pairs from different pop. Both samples are potentially problems. With defautl, the function will not keep one sample in the duplicate pair. @@ -111,9 +113,7 @@

    Arguments

    Value

    - - -

    A list with blacklisted duplicates. Write the blacklist in the working +

    A list with blacklisted duplicates. Write the blacklist in the working directory.

    @@ -133,15 +133,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/replace_by_na.html b/docs/reference/replace_by_na.html index 445ecfc5..57fac792 100644 --- a/docs/reference/replace_by_na.html +++ b/docs/reference/replace_by_na.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    replace_by_na

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reset_filters.html b/docs/reference/reset_filters.html index 02b65ed3..9336c7ef 100644 --- a/docs/reference/reset_filters.html +++ b/docs/reference/reset_filters.html @@ -4,7 +4,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -100,7 +100,9 @@

    Reset filters (individuals and markers) in radiator GDS object.

    Arguments

    -
    gds
    + + +
    gds

    (2 options) A Genomic Data Structure (GDS) file or object

    How to get GDS ? Look into tidy_genomic_data, @@ -108,97 +110,97 @@

    Arguments

    tidy_vcf or write_gds.

    -
    list.filters
    +
    list.filters

    filters (logical, optional) List current active filters for individuals and markers. Default: list.filters = TRUE.

    -
    reset.all
    +
    reset.all

    (logical, optional) Reset all individuals and markers filters. Default: reset.all = FALSE.

    -
    filter.individuals.missing
    +
    filter.individuals.missing

    (logical, optional) Default: filter.individuals.missing = FALSE.

    -
    filter.individuals.heterozygosity
    +
    filter.individuals.heterozygosity

    (logical, optional) Default: filter.individuals.heterozygosity = FALSE.

    -
    filter.individuals.coverage.total
    +
    filter.individuals.coverage.total

    (logical, optional) Default: filter.individuals.coverage.total = FALSE.

    -
    detect.mixed.genomes
    +
    detect.mixed.genomes

    (logical, optional) Default: detect.mixed.genomes = FALSE.

    -
    detect.duplicate.genomes
    +
    detect.duplicate.genomes

    (logical, optional) Default: detect.duplicate.genomes = FALSE.

    -
    filter.reproducibility
    +
    filter.reproducibility

    (logical, optional) Default: filter.reproducibility = FALSE.

    -
    filter.monomorphic
    +
    filter.monomorphic

    (logical, optional) Default: filter.monomorphic = FALSE.

    -
    filter.common.markers
    +
    filter.common.markers

    (logical, optional) Default: filter.common.markers = FALSE.

    -
    filter.ma
    +
    filter.ma

    (logical, optional) Default: filter.ma = FALSE.

    -
    filter.mean.coverage
    +
    filter.mean.coverage

    (logical, optional) Default: filter.mean.coverage = FALSE.

    -
    filter.genotyping
    +
    filter.genotyping

    (logical, optional) Default: filter.genotyping = FALSE.

    -
    filter.snp.position.read
    +
    filter.snp.position.read

    (logical, optional) Default: filter.snp.position.read = FALSE.

    -
    filter.snp.number
    +
    filter.snp.number

    (logical, optional) Default: filter.snp.number = FALSE.

    -
    filter.short.ld
    +
    filter.short.ld

    (logical, optional) Default: filter.short.ld = FALSE.

    -
    filter.long.ld
    +
    filter.long.ld

    (logical, optional) Default: filter.long.ld = FALSE.

    -
    filter.hwe
    +
    filter.hwe

    (logical, optional) Default: filter.hwe = FALSE.

    -
    filter.whitelist
    +
    filter.whitelist

    (logical, optional) Default: filter.whitelist = FALSE.

    @@ -214,14 +216,14 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # List active filters for individuals and markers
 reset_filters(gds)
 
 # You changed your decision concerning the genotyping threshold or
 # entered the wrong one:
 reset_filters(gds, filter.genotyping = TRUE)
-}
+} # }
    @@ -236,15 +238,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/run_bayescan.html b/docs/reference/run_bayescan.html index 836bd611..b33e0d05 100644 --- a/docs/reference/run_bayescan.html +++ b/docs/reference/run_bayescan.html @@ -17,7 +17,7 @@ - +
    @@ -48,7 +48,7 @@
    • - +
    @@ -114,7 +114,9 @@

    Run BayeScan

    Arguments

    -
    data
    + + +
    data

    (character, path) Read carefully because there's 2 ways.

    1. Path to BayeScan input file. To get this input rapidly: write_bayescan if you already have a tidy data, or use genomic_converter

      2. @@ -128,33 +130,33 @@

      Arguments

    -
    n
    +
    n

    (integer) Number of outputted iterations. Default: n = 5000.

    -
    thin
    +
    thin

    (integer) Thinning interval size. Default: thin = 10

    -
    nbp
    +
    nbp

    (integer) Number of pilot runs. Default: nbp = 20.

    -
    pilot
    +
    pilot

    (integer) Length of pilot runs. Default: pilot = 5000.

    -
    burn
    +
    burn

    (integer) Burn-in length. Default: burn = 50000.

    -
    pr_odds
    +
    pr_odds

    (integer) Prior odds for the neutral model. A pr_odds = 10, indicates that the neutral model is 10 times more likely than the model with selection. Larger pr_odds the more conservative is the results.

    -
    subsample
    +
    subsample

    (Integer or character) With subsample = 36, 36 individuals in each populations are chosen randomly to represent the dataset. With subsample = "min", the @@ -162,7 +164,7 @@

    Arguments

    Default is no subsampling, subsample = NULL.

    -
    iteration.subsample
    +
    iteration.subsample

    (Integer) The number of iterations to repeat subsampling. With subsample = 20 and iteration.subsample = 10, @@ -170,32 +172,22 @@

    Arguments

    Default: iteration.subsample = 1.

    -
    parallel.core
    +
    parallel.core

    (integer) Number of CPU for parallel computations. Default: parallel.core = parallel::detectCores() - 1

    -
    bayescan.path
    +
    bayescan.path

    (character, path) Provide the FULL path to BayeScan program. Default: bayescan.path = "/usr/local/bin/bayescan". See details.

    Value

    - - -

    For specific BayeScan

    - - -

    output files, see BayeScan

    - - -

    documentation, please read the manual.

    - - +

    For specific BayeScan +output files, see BayeScan +documentation, please read the manual.

    radiator::run_bayescan outputs without subsampling:

    - -

    1. bayescan: dataframe with results of BayeScan analysis.

    2. selection.summary: dataframe showing the number of markers in the different group of selections and model choice.

    3. whitelist.markers.positive.selection: Whitelist of markers under diversifying selection and common in all iterations.

      4. @@ -213,8 +205,6 @@

      Value

    4. accuracy.snp.number.plot: the plot showing the proportion of accurate/not accurate locus in relation to SNPs per locus.

    5. not.accurate.summary: dataframe summarizing the number of not accurate locus with selection type found on locus.

    radiator::run_bayescan outputs WITH subsampling:

    - -

    1. subsampling.individuals: dataframe with indivuals subsample id and random seed number.

    2. bayescan.all.subsamples: long dataframe with combined iterations of bayescan results.

    3. selection.accuracy: dataframe with all markers with selection grouping and number of times observed throughout iterations.

      4. @@ -275,7 +265,7 @@

      See also

      Examples

      - 
      if (FALSE) {
+    
      if (FALSE) { # \dontrun{
 # library(radiator)
 # get a tidy data frame and a bayescan file with radiator::genomic_converter:
 # to run with a vcf haplotype file
@@ -311,7 +301,7 @@ 
      Examples
      
 # (e.g. pop1 N = 36, pop2 N = 50 and pop3 N = 15, the subsampling will use 15
 # individuals in each pop, taken randomly.
 # You can also choose a specific subsample value with the argument.
-}
+} # }
      @@ -326,15 +316,15 @@

      Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/separate_gt.html b/docs/reference/separate_gt.html index 98c03ad7..746d5fd6 100644 --- a/docs/reference/separate_gt.html +++ b/docs/reference/separate_gt.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -99,15 +99,15 @@

    separate_gt

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/separate_markers.html b/docs/reference/separate_markers.html index 971ae215..2ee372b3 100644 --- a/docs/reference/separate_markers.html +++ b/docs/reference/separate_markers.html @@ -9,7 +9,7 @@ - +
    @@ -40,7 +40,7 @@
    • - +
    @@ -99,7 +99,9 @@

    Separate markers column into chrom, locus and pos

    Arguments

    -
    data
    + + +
    data

    An object with a column named MARKERS. If CHROM, LOCUS, POS are already present, the function returns the dataset untouched. @@ -107,7 +109,7 @@

    Arguments

    radiator GDS object.

    -
    sep
    +
    sep

    (optional, character) Separator used to identify the different field in the MARKERS column.

    When the MARKERS column doesn't have separator and the function is used @@ -116,7 +118,7 @@

    Arguments

    Default: sep = "__".

    -
    markers.meta.lists.only
    +
    markers.meta.lists.only

    (logical, optional) Allows to keep only the markers metadata: "VARIANT_ID", "MARKERS", "CHROM", "LOCUS", "POS", useful for whitelist @@ -124,7 +126,7 @@

    Arguments

    Default: markers.meta.lists.only = FALSE

    -
    markers.meta.all.only
    +
    markers.meta.all.only

    (logica, optionall) Allows to keep all available markers metadata: "VARIANT_ID", "MARKERS", "CHROM", "LOCUS", "POS", "COL", "REF", "ALT", @@ -132,14 +134,14 @@

    Arguments

    Default: markers.meta.all.only = FALSE

    -
    generate.markers.metadata
    +
    generate.markers.metadata

    (logical, optional) Generate missing markers metadata when missing. "CHROM", "LOCUS", "POS". Default: generate.markers.metadata = TRUE

    -
    generate.ref.alt
    +
    generate.ref.alt

    (logical, optional) Generate missing REF/ALT alleles with: REF = A and ALT = C (for biallelic datasets, only). It is turned off automatically @@ -148,7 +150,7 @@

    Arguments

    Default: generate.ref.alt = FALSE

    -
    biallelic
    +
    biallelic

    (logical) Speed up the function execution by entering if the dataset is biallelic or not. Used internally for verification, before generating REF/ALT info. @@ -158,13 +160,13 @@

    Arguments

    Default: biallelic = NULL

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -172,9 +174,7 @@

    Arguments

    Value

    - - -

    The same data in the global environment, with 3 new columns: +

    The same data in the global environment, with 3 new columns: CHROM, LOCUS, POS. Additionnal columns may be genrated, see arguments documentation.

    @@ -189,10 +189,10 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 whitelist <- radiator::separate_markers(data = whitelist.markers)
 tidy.data <- radiator::separate_markers(data = bluefintuna.data)
-}
+} # }
    @@ -207,15 +207,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/sex_markers_plot.html b/docs/reference/sex_markers_plot.html index 51a4a87a..eee06383 100644 --- a/docs/reference/sex_markers_plot.html +++ b/docs/reference/sex_markers_plot.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -105,15 +105,15 @@

    sex_markers_plot

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/sexy_markers.html b/docs/reference/sexy_markers.html index 48937ad3..7e876408 100644 --- a/docs/reference/sexy_markers.html +++ b/docs/reference/sexy_markers.html @@ -8,7 +8,7 @@ - +
    @@ -39,7 +39,7 @@
    • - +
    @@ -98,20 +98,22 @@

    sexy_markers finds sex-linked markers and re-assigns sex

    Arguments

    -
    data
    + + +
    data

    (object or file) DArT file .csv or .tsv, VCF file .vcf, GDS file or object (.gds).
    See read_dart or read_vcf for more details.

    -
    silicodata
    +
    silicodata

    (optional, file) A silico (dominant marker) DArT file .csv or .tsv.
    This can be count or genotyped data. Note that both data and silicodata can be used at the same time.
    Default: silicodata = NULL.

    -
    strata
    +
    strata

    (file) A tab delimited file with a minimum of 2 columns (INDIVIDUALS, STRATA) for VCF files and 3 columns for DArT files (TARGET_ID, INDIVIDUALS, STRATA).

    -
    boost.analysis
    +
    boost.analysis

    (optional, logical) This method uses machine learning approaches to find sex markers and re-assign samples in sex group.
    The approach is currently under construction. Default: boost.analysis = FALSE.

    -
    coverage.thresholds
    +
    coverage.thresholds

    (optional, integer) The minimum coverage required to call a marker absent. For silico genotype data this must be < 1.
    Default: coverage.thresholds = 1.

    -
    filters
    +
    filters

    (optional, logical) When filters = TRUE, the data will be filtered for monomorphic loci, missingness of individuals and heterozygosity of individuals.
    CAUTION: we advice to use these filter, since not filtering or filtering too @@ -146,25 +148,25 @@

    Arguments

    Default: filters = TRUE.

    -
    interactive.filter
    +
    interactive.filter

    (optional, logical) When interactive.filter = TRUE the function will ask for your input to define thresholds. If interactive.filter = FALSE the function expects additional arguments (see Advance mode).
    Default: interactive.filter = TRUE.

    -
    folder.name
    +
    folder.name

    (optional,character) Name of the folder to store the results. Default: folder.name = NULL. The name sexy_markers_datetime will be generated.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -172,9 +174,7 @@

    Arguments

    Value

    - - -

    The created object contains:

    1. A list with (1) the summarised SNP data per sex and +

      The created object contains:

      1. A list with (1) the summarised SNP data per sex and (2) the summarised silico data per sex. This should allow you to re-create the various plots.

      2. A vector with the names of the sex-linked marker. One vector for each sex method.

      3. A dataframe with a summary of the sex-linked markers and their sequence (if available).

        4. @@ -190,7 +190,7 @@

        Details

    Assumptions

    - +

    1. Genetic Sex Determination System over a e.g. environmental-sex-determination system.

    2. Genome coverage: restriction sites randomly spread throughout the whole genome.

      3. @@ -205,7 +205,7 @@

      Assumptions

    Prerequisites

    - +

    1. Sample size: Ideally, the data must have enough individuals (n > 100).

    2. Batch effect: Sex should be randomized on lanes/chips during sequencing.

      3. @@ -226,7 +226,7 @@

      Prerequisites

    Sex methods

    - +

    Heterogametic sex-markers:

    • Presence/Absence method: To identify markers on Y or W chromosomes, we look at the presence or @@ -247,7 +247,7 @@

      Sex methods

    Advance mode

    - +

    dots-dots-dots ... allows to pass several arguments for fine-tuning the function:

    • species: To give your figures some meanings. @@ -289,7 +289,7 @@

      Advance mode

    Life cycle

    - +

    Machine Learning approaches (Random Forest and Extreme Gradient Boosting Trees) @@ -308,13 +308,13 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # The minimum
 sex.markers <- radiator::sexy_markers(
     data = "shark.dart.data.csv",
     strata = "shark.strata.tsv")
 # This will use the default: interactive version and a list is created and to view the sex markers
-}
+} # }
    @@ -329,15 +329,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/simulate_genos_from_posterior.html b/docs/reference/simulate_genos_from_posterior.html index 609cc892..13e65e38 100644 --- a/docs/reference/simulate_genos_from_posterior.html +++ b/docs/reference/simulate_genos_from_posterior.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -81,15 +81,17 @@

    simulate_genos_from_posterior

    Arguments

    -
    D
    + + +
    D

    an 012,-1 matrix of observed genotypes

    -
    p
    +
    p

    the estimated allele freqs

    -
    m
    +
    m

    the genotyping error rate (must be a scalar)

    @@ -110,15 +112,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/split_tibble_rows.html b/docs/reference/split_tibble_rows.html index 2d7ca63b..ab2fe90b 100644 --- a/docs/reference/split_tibble_rows.html +++ b/docs/reference/split_tibble_rows.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -93,15 +93,15 @@

    split_tibble_rows

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/split_vcf.html b/docs/reference/split_vcf.html index 5c14343d..de9b2166 100644 --- a/docs/reference/split_vcf.html +++ b/docs/reference/split_vcf.html @@ -4,7 +4,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -79,7 +79,9 @@

    Split a VCF file

    Arguments

    -
    data
    + + +
    data

    14 options for input (diploid data only): VCFs (SNPs or Haplotypes, to make the vcf population ready), plink (tped, bed), stacks haplotype file, genind (library(adegenet)), @@ -95,7 +97,7 @@

    Arguments

    to understand it's limit before asking raditor to convert or filter your dataset.

    -
    strata
    +
    strata

    A file identical to the strata file usually used in radiator, with an additional column named: SPLIT. This new column contains numerical values @@ -105,21 +107,19 @@

    Arguments

    SPLIT, above this would result in 3 VCF files created).

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    ...
    +
    ...

    (optional) To pass further arguments for fine-tuning the function.

    Value

    - - -

    The function returns in the global environment a list with +

    The function returns in the global environment a list with the different tidy dataset from the split vcf. In the working directory, the splitted VCF files with "_1", "_2" in the name.

    @@ -130,13 +130,13 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 split.data <- radiator::split_vcf(
 data = "batch_1.vcf",
 strata = "strata.split.tsv",
 blacklist.id = "blacklisted.id.txt",
 whitelist.markers = "whitelist.loci.txt")
-}
+} # }
    @@ -151,15 +151,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/strata_haplo.html b/docs/reference/strata_haplo.html index e20040bc..d0dc5c3d 100644 --- a/docs/reference/strata_haplo.html +++ b/docs/reference/strata_haplo.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    strata_haplo

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/subsampling_data.html b/docs/reference/subsampling_data.html index d0e9413e..15039acd 100644 --- a/docs/reference/subsampling_data.html +++ b/docs/reference/subsampling_data.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -93,15 +93,15 @@

    subsampling data

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/summarise_genotypes.html b/docs/reference/summarise_genotypes.html index 0add851b..046c34cb 100644 --- a/docs/reference/summarise_genotypes.html +++ b/docs/reference/summarise_genotypes.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -92,15 +92,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/summarize_sex.html b/docs/reference/summarize_sex.html index 693cb631..83a20cd3 100644 --- a/docs/reference/summarize_sex.html +++ b/docs/reference/summarize_sex.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -94,15 +94,15 @@

    summarize_sex

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/summary_gds.html b/docs/reference/summary_gds.html index 55233e9a..8d348cb1 100644 --- a/docs/reference/summary_gds.html +++ b/docs/reference/summary_gds.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -77,7 +77,9 @@

    summary_gds

    Arguments

    -
    gds
    + + +
    gds

    (2 options) A Genomic Data Structure (GDS) file or object

    How to get GDS ? Look into tidy_genomic_data, @@ -85,12 +87,12 @@

    Arguments

    tidy_vcf or write_gds.

    -
    check.sync
    +
    check.sync

    (logical, optional) Check if GDS object is in sync with radiator metada.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -109,15 +111,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/summary_rad.html b/docs/reference/summary_rad.html index d5523a7c..1de1df76 100644 --- a/docs/reference/summary_rad.html +++ b/docs/reference/summary_rad.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Summary statistics for RADseq data

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -92,16 +94,16 @@

    Arguments

    tidy_vcf.

    -
    path.folder
    +
    path.folder

    (path, optional) By default will print results in the working directory. Default: path.folder = NULL.

    -
    digits
    +
    digits

    (integer, optional). Default: digits = 4.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -120,15 +122,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/summary_strata.html b/docs/reference/summary_strata.html index e6c4b2a6..11461d77 100644 --- a/docs/reference/summary_strata.html +++ b/docs/reference/summary_strata.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -81,13 +81,14 @@

    Summary of strata

    Arguments

    -
    strata
    + + +
    strata

    (path or object) The strata file or object.

    Value

    -

    1. Number of strata/populations

    2. Number of individuals

      3. @@ -103,9 +104,9 @@

      See also

      Examples

      - 
      if (FALSE) {
+    
      if (FALSE) { # \dontrun{
 radiator::summary_strata(strata)
-}
+} # }
      @@ -120,15 +121,15 @@

      Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/switch_allele_count.html b/docs/reference/switch_allele_count.html index c8f9e6a5..9ad10116 100644 --- a/docs/reference/switch_allele_count.html +++ b/docs/reference/switch_allele_count.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    switch_allele_count

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/switch_genotypes.html b/docs/reference/switch_genotypes.html index 762b708d..b5803968 100644 --- a/docs/reference/switch_genotypes.html +++ b/docs/reference/switch_genotypes.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    switch_genotypes

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/sync_gds.html b/docs/reference/sync_gds.html index ebe527e2..4748d2c5 100644 --- a/docs/reference/sync_gds.html +++ b/docs/reference/sync_gds.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -89,37 +89,39 @@

    sync_gds

    Arguments

    -
    gds
    + + +
    gds

    The gds object.

    -
    samples
    +
    samples

    (optional, character string). Will sync the gds object/file with these samples. With default, uses the individuals in the radiator node. If not found, goes a level above and uses the individuals in the main GDS. Default: samples = NULL.

    -
    variant.id
    +
    variant.id

    (optional, integer string). Will sync the gds object/file with these variant.id With default, uses the variant.id in the radiator node. If not found, goes a level above and uses the variant.id in the main GDS. Default: variant.id = NULL.

    -
    reset.gds
    +
    reset.gds

    (optional, logical) Default: reset.gds = FALSE.

    -
    reset.filters.m
    +
    reset.filters.m

    (optional, logical) To reset only markers/variant. Default: reset.filters.m = FALSE.

    -
    reset.filters.i
    +
    reset.filters.i

    (optional, logical) To reset only individuals. Default: reset.filters.i = FALSE.

    -
    verbose
    +
    verbose

    (optional, logical) Default: verbose = FALSE.

    @@ -140,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/tibble_stats.html b/docs/reference/tibble_stats.html index bf32c3cd..0a4692b5 100644 --- a/docs/reference/tibble_stats.html +++ b/docs/reference/tibble_stats.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    tibble_stats

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/tidy2gds.html b/docs/reference/tidy2gds.html index c2e5b740..c2b3f1f7 100644 --- a/docs/reference/tidy2gds.html +++ b/docs/reference/tidy2gds.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    tidy2gds

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/tidy2wide.html b/docs/reference/tidy2wide.html index 8fd58654..d41e0843 100644 --- a/docs/reference/tidy2wide.html +++ b/docs/reference/tidy2wide.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -96,15 +96,15 @@

    tidy2wide

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/tidy_dart_metadata.html b/docs/reference/tidy_dart_metadata.html index 58a83da3..a9896d41 100644 --- a/docs/reference/tidy_dart_metadata.html +++ b/docs/reference/tidy_dart_metadata.html @@ -7,7 +7,7 @@ - +
    @@ -38,7 +38,7 @@
    • - +
    @@ -90,14 +90,16 @@

    Import and tidy

    Arguments

    -
    data
    + + +
    data

    DArT output file. Note that most popular formats used by DArT are recognised (1- and 2- row format, also called binary, and count data.). If you encounter a problem, sent me your data so that I can update the function. The function can import .csv or .tsv files.

    -
    filename
    +
    filename

    (optional) The function uses write.fst, to write the tidy data frame in the working directory. The file extension appended to @@ -106,13 +108,13 @@

    Arguments

    in the global environment only (i.e. not written in the working directory...).

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    @@ -120,9 +122,7 @@

    Arguments

    Value

    - - -

    A tidy dataframe with these columns:

    1. MARKERS: generated by radiator and correspond to CHROM + LOCUS + POS +

      A tidy dataframe with these columns:

      1. MARKERS: generated by radiator and correspond to CHROM + LOCUS + POS separated by 2 underscores.

      2. CHROM: the chromosome, for de novo: CHROM_1.

      3. LOCUS: the locus.

        4. @@ -141,11 +141,11 @@

        Author

        Examples

        - 
        if (FALSE) {
+    
        if (FALSE) { # \dontrun{
 clownfish.dart.tidy <- radiator::tidy_dart_metadata(
 data = "clownfish.dart.tsv",
 verbose = TRUE)
-}
+} # }
        @@ -160,15 +160,15 @@

        Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/tidy_fstat.html b/docs/reference/tidy_fstat.html index b28d279e..b5669367 100644 --- a/docs/reference/tidy_fstat.html +++ b/docs/reference/tidy_fstat.html @@ -11,7 +11,7 @@ - +
    @@ -42,7 +42,7 @@
    • - +
    @@ -93,12 +93,14 @@

    fstat file to tidy dataframe

    Arguments

    -
    data
    + + +
    data

    A fstat filename with extension .dat.

    -
    strata
    +
    strata

    (optional) A tab delimited file with 2 columns. Header: INDIVIDUALS and STRATA. The STRATA column can be any hierarchical grouping. @@ -106,14 +108,14 @@

    Arguments

    Default: strata = NULL.

    -
    tidy
    +
    tidy

    (optional, logical) With tidy = FALSE, the markers are the variables and the genotypes the observations (wide format). With the default: tidy = TRUE, markers and genotypes are variables with their own columns (long format).

    -
    filename
    +
    filename

    (optional) The file name for the tidy data frame written to the working directory. Default: filename = NULL, the tidy data is @@ -122,9 +124,7 @@

    Arguments

    Value

    - - -

    The output in your global environment is a wide or long/tidy data frame. +

    The output in your global environment is a wide or long/tidy data frame. If filename is provided, the wide or long/tidy data frame is also written to the working directory.

    @@ -145,7 +145,7 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # We will use the fstat dataset provided with adegenet package
 require("hierfstat")
 
@@ -165,7 +165,7 @@ 
    Examples
    
     ),
 tidy = FALSE
 )
-}
+} # }
    @@ -180,15 +180,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/tidy_genepop.html b/docs/reference/tidy_genepop.html index d2f61ecb..39ac8811 100644 --- a/docs/reference/tidy_genepop.html +++ b/docs/reference/tidy_genepop.html @@ -11,7 +11,7 @@ - +
    @@ -42,7 +42,7 @@
    • - +
    @@ -93,12 +93,14 @@

    Import genepop file and convert to a tidy dataframe

    Arguments

    -
    data
    + + +
    data

    A genepop filename with extension .gen.

    -
    strata
    +
    strata

    (optional) A tab delimited file with 2 columns. Header: INDIVIDUALS and STRATA. The STRATA column can be any hierarchical grouping. @@ -106,14 +108,14 @@

    Arguments

    Default: strata = NULL.

    -
    tidy
    +
    tidy

    (optional, logical) With tidy = FALSE, the markers are the variables and the genotypes the observations (wide format). With the default: tidy = TRUE, markers and genotypes are variables with their own columns (long format).

    -
    filename
    +
    filename

    (optional) The file name for the tidy data frame written to the working directory. Default: filename = NULL, the tidy data is @@ -122,9 +124,7 @@

    Arguments

    Value

    - - -

    The output in your global environment is a wide or long/tidy data frame. +

    The output in your global environment is a wide or long/tidy data frame. If filename is provided, the wide or long/tidy data frame is also written to the working directory.

    @@ -218,7 +218,7 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # We will use the genepop dataset provided with adegenet package
 require("adegenet")
 
@@ -238,7 +238,7 @@ 
    Examples
    
 ),
     tidy = FALSE
 )
-}
+} # }
    @@ -253,15 +253,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/tidy_genind.html b/docs/reference/tidy_genind.html index 73350613..9f3a2000 100644 --- a/docs/reference/tidy_genind.html +++ b/docs/reference/tidy_genind.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,29 +83,31 @@

    Tidy a genind object to a tidy dataframe

    Arguments

    -
    data
    + + +
    data

    (path or object) A genind object in the global environment or path to a genind file that will be open with readRDS.

    -
    tidy
    +
    tidy

    (logical) Generate a tidy dataset. Default: tidy = TRUE.

    -
    gds
    +
    gds

    (optional, logical) To write a radiator gds object. Currently, for biallelic datasets only. Default: gds = TRUE.

    -
    write
    +
    write

    (optional, logical) To write in the working directory the tidy data. The file is written with radiator_genind_DATE@TIME.rad. Default: write = FALSE.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -151,15 +153,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/tidy_genlight.html b/docs/reference/tidy_genlight.html index 18ef4e35..f7e7a7d5 100644 --- a/docs/reference/tidy_genlight.html +++ b/docs/reference/tidy_genlight.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -88,34 +88,36 @@

    Tidy a genlight object to a tidy dataframe and/or GDS object/file

    Arguments

    -
    data
    + + +
    data

    (path or object) A genlight object in the global environment or path to a genlight file that will be open with readRDS.

    -
    tidy
    +
    tidy

    (logical) Generate a tidy dataset. Default: tidy = TRUE.

    -
    gds
    +
    gds

    (optional, logical) To write a radiator gds object. Default: gds = TRUE.

    -
    write
    +
    write

    (optional, logical) To write in the working directory the tidy data. The file is written with radiator_genlight_DATE@TIME.rad. Default: write = FALSE.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    @@ -158,15 +160,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/tidy_genomic_data.html b/docs/reference/tidy_genomic_data.html index c2181815..40d40817 100644 --- a/docs/reference/tidy_genomic_data.html +++ b/docs/reference/tidy_genomic_data.html @@ -12,7 +12,7 @@ - +
    @@ -43,7 +43,7 @@
    • - +
    @@ -102,7 +102,9 @@

    Transform common genomic dataset format in a tidy data frame

    Arguments

    -
    data
    + + +
    data

    14 options for input (diploid data only): VCFs (SNPs or Haplotypes, to make the vcf population ready), plink (tped, bed), stacks haplotype file, genind (library(adegenet)), @@ -118,7 +120,7 @@

    Arguments

    to understand it's limit before asking raditor to convert or filter your dataset.

    -
    strata
    +
    strata

    (optional) The strata file is a tab delimited file with a minimum of 2 columns headers: INDIVIDUALS and STRATA. Documented in read_strata. @@ -128,7 +130,7 @@

    Arguments

    Default: strata = NULL.

    -
    filename
    +
    filename

    (optional) The function uses write.fst, to write the tidy data frame in the working directory. The file extension appended to @@ -137,27 +139,25 @@

    Arguments

    in the global environment only (i.e. not written in the working directory...).

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) To pass further arguments for fine-tuning the function.

    Value

    - - -

    The output in your global environment is a tidy data frame. +

    The output in your global environment is a tidy data frame. If filename is provided, the tidy data frame is also written in the working directory with file extension .rad. The file is written with the @@ -166,7 +166,7 @@

    Value

    Input genomic datasets

    - +

    1. VCF files must end with .vcf: documented in tidy_vcf

    2. PLINK files must end with .tped or .bed: documented in tidy_plink

      3. @@ -189,7 +189,7 @@

      Input genomic datasets

    Advance mode

    - +

    dots-dots-dots ... allows to pass several arguments for fine-tuning the function:

    1. vcf.metadata (optional, logical or string). @@ -222,7 +222,7 @@

      Author

      Examples

      - 
      if (FALSE) {
+    
      if (FALSE) { # \dontrun{
 #To verify your file is detected by radiator as the correct format:
 radiator::detect_genomic_format(data = "populations.snps.vcf")
 
@@ -232,7 +232,7 @@ 
      Examples
      
 tidy.vcf <- tidy_genomic_data(
    data = "populations.snps.vcf", strata = "strata.treefrog.tsv",
    whitelist.markers = "whitelist.vcf.txt")
-}
+} # }
      @@ -247,15 +247,15 @@

      Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/tidy_gtypes.html b/docs/reference/tidy_gtypes.html index f2e71c88..fd22d05c 100644 --- a/docs/reference/tidy_gtypes.html +++ b/docs/reference/tidy_gtypes.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Tidy a gtypes object to a tidy dataframe

    Arguments

    -
    data
    + + +
    data

    A gtypes object (>= v.2.0.2) in the global environment.

    @@ -111,15 +113,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/tidy_plink.html b/docs/reference/tidy_plink.html index c4c3c96f..4c3acc3a 100644 --- a/docs/reference/tidy_plink.html +++ b/docs/reference/tidy_plink.html @@ -7,7 +7,7 @@ - +
    @@ -38,7 +38,7 @@
    • - +
    @@ -90,7 +90,9 @@

    Tidy PLINK tped and bed files

    Arguments

    -
    data
    + + +
    data

    The PLINK file.

    • bi-allelic data only. For haplotypes use VCF.

    • tped file format: the corresponding tfam file must be in the directory.

    • bed file format: IS THE PREFERRED format, the corresponding @@ -98,19 +100,19 @@

      Arguments

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -118,13 +120,11 @@

    Arguments

    Value

    - - -

    A tidy tibble of the PLINK file.

    +

    A tidy tibble of the PLINK file.

    Advance mode

    - +

    dots-dots-dots ... allows to pass several arguments for fine-tuning the function:

    1. calibrate.alleles: logical. For tped files, if @@ -136,7 +136,7 @@

      Advance mode

      References

      Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir BS, -Laurie C, Levine D (2017). SeqArray -- A storage-efficient high-performance +Laurie C, Levine D (2017). SeqArray – A storage-efficient high-performance data format for WGS variant calls. Bioinformatics.

      PLINK: a tool set for whole-genome association and population-based linkage @@ -155,13 +155,13 @@

      Author

      Examples

      - 
      if (FALSE) {
+    
      if (FALSE) { # \dontrun{
 data <- radiator::tidy_plink(data = "my_plink_file.bed", verbose = TRUE)
 
 
 # when conversion is required from TPED to BED, in Terminal:
 # plink --tfile my_plink_file --make-bed --allow-no-sex --allow-extra-chr --chr-set 95
-}
+} # }
      @@ -176,15 +176,15 @@

      Examples

      -

      Site built with pkgdown 2.0.9.

      +

      Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/tidy_vcf.html b/docs/reference/tidy_vcf.html index 140379e4..7a9d3df9 100644 --- a/docs/reference/tidy_vcf.html +++ b/docs/reference/tidy_vcf.html @@ -10,7 +10,7 @@ - +
    @@ -41,7 +41,7 @@
    • - +
    @@ -98,12 +98,14 @@

    Tidy vcf file

    Arguments

    -
    data
    + + +
    data

    (VCF file, character string) The VCF SNPs are biallelic or haplotypes. To make the VCF population-ready, the argument strata is required.

    -
    strata
    +
    strata

    (optional) The strata file is a tab delimited file with a minimum of 2 columns headers: INDIVIDUALS and STRATA. Documented in read_strata. @@ -113,7 +115,7 @@

    Arguments

    Default: strata = NULL.

    -
    filename
    +
    filename

    (optional) The function uses write.fst, to write the tidy data frame in the working directory. The file extension appended to @@ -122,33 +124,31 @@

    Arguments

    in the global environment only (i.e. not written in the working directory...).

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    ...
    +
    ...

    (optional) To pass further argument for fine-tuning the tidying (read below).

    Value

    - - -

    The output in your global environment is a tidy data frame, the GDS file +

    The output in your global environment is a tidy data frame, the GDS file generated is in the working directory under the name given during function execution.

    VCF file format

    - +

    PLINK: radiator fills the LOCUS column of PLINK VCFs with @@ -180,7 +180,7 @@

    VCF file format

    Advance mode, using dots-dots-dots ...

    - +

    The arguments below are not available using code completion (e.g. with TAB), @@ -296,7 +296,7 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # very basic with built-in defaults (not recommended):
 prep.data <- radiator::tidy_vcf(data = "populations.snps.vcf")
 
@@ -311,7 +311,7 @@ 
    Examples
    
     filter.short.ld = "mac",
     path.folder = "salamander/prep_data",
     verbose = TRUE)
-}
+} # }
    @@ -326,15 +326,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/tidy_wide.html b/docs/reference/tidy_wide.html index ea440e02..38ec135a 100644 --- a/docs/reference/tidy_wide.html +++ b/docs/reference/tidy_wide.html @@ -7,7 +7,7 @@ - +
    @@ -38,7 +38,7 @@
    • - +
    @@ -85,7 +85,9 @@

    Read/Import a tidy genomic data frames.

    Arguments

    -
    data
    + + +
    data

    A file in the working directory or object in the global environment in wide or long (tidy) formats. See details for more info.

    How to get a tidy data frame ? @@ -93,7 +95,7 @@

    Arguments

    tidy_genomic_data.

    -
    import.metadata
    +
    import.metadata

    (optional, logical) With import.metadata = TRUE the metadata (anything else than the genotype) will be imported for the long format exclusively. Default: import.metadata = FALSE, no metadata.

    @@ -101,9 +103,7 @@

    Arguments

    Value

    - - -

    A tidy data frame in the global environment.

    +

    A tidy data frame in the global environment.

    Details

    @@ -160,15 +160,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/update_bl_individuals.html b/docs/reference/update_bl_individuals.html index 992f6399..f12f164f 100644 --- a/docs/reference/update_bl_individuals.html +++ b/docs/reference/update_bl_individuals.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -94,15 +94,15 @@

    update_bl_individuals

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/update_bl_markers.html b/docs/reference/update_bl_markers.html index 9a0d14af..39ce5525 100644 --- a/docs/reference/update_bl_markers.html +++ b/docs/reference/update_bl_markers.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -94,15 +94,15 @@

    update_bl_markers

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/update_filter_parameter.html b/docs/reference/update_filter_parameter.html index 0966161b..a0e0dd8d 100644 --- a/docs/reference/update_filter_parameter.html +++ b/docs/reference/update_filter_parameter.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -99,15 +99,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/update_radiator_gds.html b/docs/reference/update_radiator_gds.html index 7245a4c1..e0c00342 100644 --- a/docs/reference/update_radiator_gds.html +++ b/docs/reference/update_radiator_gds.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -97,15 +97,15 @@

    update_radiator_gds

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/vcf_strata.html b/docs/reference/vcf_strata.html index 8f19ed9c..11d57f28 100644 --- a/docs/reference/vcf_strata.html +++ b/docs/reference/vcf_strata.html @@ -4,7 +4,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -79,11 +79,13 @@

    Join stratification metadata to a VCF (population-aware VCF)

    Arguments

    -
    data
    + + +
    data

    A VCF file

    -
    strata
    +
    strata

    (optional) A tab delimited file at least 2 columns with header: INDIVIDUALS and STRATA. @@ -91,7 +93,7 @@

    Arguments

    To create a strata file see individuals2strata.

    -
    filename
    +
    filename

    (optional) The file name for the modifed VCF, written to the working directory. Default: filename = NULL will make a custom filename with data and time.

    @@ -99,9 +101,7 @@

    Arguments

    Value

    - - -

    A VCF file in the working directory with new FORMAT field(s) +

    A VCF file in the working directory with new FORMAT field(s) correponding to the strata column(s).

    @@ -132,15 +132,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_arlequin.html b/docs/reference/write_arlequin.html index 323b789d..c10aff1d 100644 --- a/docs/reference/write_arlequin.html +++ b/docs/reference/write_arlequin.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,33 +83,33 @@

    Write an arlequin file from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    pop.levels
    +
    pop.levels

    (optional, string) A character string with your populations ordered. Default: pop.levels = NULL.

    -
    filename
    +
    filename

    (optional) The file name prefix for the arlequin file written to the working directory. With default: filename = NULL, the filename generated follow this radiator_arlequin_DATE@TIME.csv.

    -
    ...
    +
    ...

    other parameters passed to the function.

    Value

    - - -

    An arlequin file is saved to the working directory.

    +

    An arlequin file is saved to the working directory.

    References

    @@ -134,15 +134,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_bayescan.html b/docs/reference/write_bayescan.html index 914e42c6..c173bb57 100644 --- a/docs/reference/write_bayescan.html +++ b/docs/reference/write_bayescan.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -89,41 +89,41 @@

    Write a

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    pop.select
    +
    pop.select

    (optional, string) Selected list of populations for the analysis. e.g. pop.select = c("QUE", "ONT") to select QUE and ONT population samples (out of 20 pops). Default: pop.select = NULL

    -
    filename
    +
    filename

    (optional) The file name prefix for the bayescan file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_bayescan_.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    ...
    +
    ...

    (optional) To pass further arguments for fine-tuning the function.

    Value

    - - -

    A bayescan file is written in the working directory.

    +

    A bayescan file is written in the working directory.

    Details

    @@ -162,15 +162,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_betadiv.html b/docs/reference/write_betadiv.html index 4ce07623..ff4730c2 100644 --- a/docs/reference/write_betadiv.html +++ b/docs/reference/write_betadiv.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Write a betadiv file from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? @@ -92,9 +94,7 @@

    Arguments

    Value

    - - -

    A betadiv object is returned.

    +

    A betadiv object is returned.

    References

    @@ -125,15 +125,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_colony.html b/docs/reference/write_colony.html index f586eeac..73a5d880 100644 --- a/docs/reference/write_colony.html +++ b/docs/reference/write_colony.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -97,7 +97,9 @@

    Write a COLONY input file

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -106,28 +108,28 @@

    Arguments

    tidy_vcf.

    -
    strata
    +
    strata

    (path or object) The strata file or object. Additional documentation is available in read_strata. Use that function to whitelist/blacklist populations/individuals. Option to set pop.levels/pop.labels is also available.

    -
    sample.markers
    +
    sample.markers

    (number) COLONY can take a long time to run, use a random subsample of your markers to speed test COLONY e.g. sample.markers = 500 to use only 500 randomly chosen markers. Default: sample.markers = NULL, will use all markers.

    -
    pop.select
    +
    pop.select

    (optional, string) Selected list of populations for the analysis. e.g. pop.select = c("QUE", "ONT") to select QUE and ONT population samples (out of 20 pops). Default: pop.select = NULL

    -
    allele.freq
    +
    allele.freq

    (optional, string) Allele frequency can be computed from a select group. e.g. allele.freq = "QUE" or allele.freq = c("QUE", "ONT"). @@ -136,82 +138,82 @@

    Arguments

    Default: allele.freq = NULL, will not compute allele frequency.

    -
    inbreeding
    +
    inbreeding

    (boolean) 0/1 no inbreeding/inbreeding. Default: inbreeding = 0

    -
    mating.sys.males
    +
    mating.sys.males

    (boolean) Mating system in males. 0/1 polygyny/monogyny. Default: mating.sys.males = 0.

    -
    mating.sys.females
    +
    mating.sys.females

    (boolean) Mating system in females. 0/1 polygyny/monogyny. Default: mating.sys.females = 0.

    -
    clone
    +
    clone

    (boolean) Should clones and duplicated individuals be inferred. 0/1, yes/no. Default: clone = 0.

    -
    run.length
    +
    run.length

    (integer) Length of run. 1 (short), 2 (medium), 3 (long), 4 (very long). Start with short or medium run and consider longer run if your estimates probability are not stable or really good. Default: run.length = 2.

    -
    analysis
    +
    analysis

    (integer) Analysis method. 0 (Pairwise-Likelihood Score), 1 (Full Likelihood), 2 (combined Pairwise-Likelihood Score and Full Likelihood). Default: analysis = 1.

    -
    allelic.dropout
    +
    allelic.dropout

    Locus allelic dropout rate. Default : allelic.dropout = 0.

    -
    error.rate
    +
    error.rate

    Locus error rate. Default:error.rate = 0.02.

    -
    print.all.colony.opt
    +
    print.all.colony.opt

    (logical) Should all COLONY options be printed in the file.

    This require manual curation, for the file to work directly with COLONY. Default = print.all.colony.opt = FALSE.

    -
    random.seed
    +
    random.seed

    (integer, optional) For reproducibility, set an integer that will be used inside the function that requires randomness. With default, a random number is generated and printed in the appropriate output. Default: random.seed = NULL.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    filename
    +
    filename

    Name of the acronym for filenaming in the working directory.

    -
    ...
    +
    ...

    (optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

    @@ -219,9 +221,7 @@

    Arguments

    Value

    - - -

    A COLONY file in your working directory (2 if you selected imputations arguments...)

    +

    A COLONY file in your working directory (2 if you selected imputations arguments...)

    Details

    @@ -254,10 +254,10 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # Simplest way to run the function with a tidy dataset:
 colony.file <- radiator::write_colony(data = "turtle.data.rad")
-}
+} # }
    @@ -272,15 +272,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_dadi.html b/docs/reference/write_dadi.html index 5add85bd..4a810a22 100644 --- a/docs/reference/write_dadi.html +++ b/docs/reference/write_dadi.html @@ -9,7 +9,7 @@ - +
    @@ -40,7 +40,7 @@
    • - +
    @@ -97,39 +97,41 @@

    Write a dadi SNP input file from a tidy data frame.

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    fasta.ingroup
    +
    fasta.ingroup

    (optional) The fasta file, sequences for the ingroup. Leave empty if no outgroup. Default: fasta.ingroup = NULL.

    -
    fasta.outgroup
    +
    fasta.outgroup

    (optional) The fasta file, sequences for the outgroup. Default: fasta.outgroup = NULL.

    -
    sumstats.ingroup
    +
    sumstats.ingroup

    (optional) The sumstats output file from STACKS when running STACKS for the ingroup fasta file.This file is required to use with an outgroup. Leave empty if no outgroup. Default: sumstats.ingroup = NULL.

    -
    sumstats.outgroup
    +
    sumstats.outgroup

    (optional) The sumstats output file from STACKS when running STACKS for the outgroup fasta file. This file is required to use an outgroup. Default: sumstats.outgroup = NULL.

    -
    dadi.input.filename
    +
    dadi.input.filename

    (optional) Name of the dadi SNP input file written to the working directory. e.g. dadi.file.tsv. Default use date and time to make the file. If used, the file extension @@ -137,7 +139,7 @@

    Arguments

    Default: dadi.input.filename = NULL.

    -
    calibrate.alleles
    +
    calibrate.alleles

    (optional, logical) To re-calibrate REF an ALT alleles. Will be done automatically to the dataset if the required genomic format is not found. Please use if you have removed individuals. @@ -146,9 +148,7 @@

    Arguments

    Value

    - - -

    The function returns tibble and the dadi input file in the working +

    The function returns tibble and the dadi input file in the working directory.

    @@ -165,7 +165,7 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # without outgroup:
 dadi.data <- radiator::write_dadi(data = "my_tidy_dataset.rad")
 
@@ -177,7 +177,7 @@ 
    Examples
    
    sumstats.ingroup = "batch_1.sumstats.ingroup.tsv",
    sumstats.outgroup = "batch_1.sumstats.outgroup.tsv"
 )
-}
+} # }
    @@ -192,15 +192,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_fasta.html b/docs/reference/write_fasta.html index 481d4206..e01ceeea 100644 --- a/docs/reference/write_fasta.html +++ b/docs/reference/write_fasta.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -88,15 +88,15 @@

    Export FASTA

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_faststructure.html b/docs/reference/write_faststructure.html index cdc21ba5..623aa6b6 100644 --- a/docs/reference/write_faststructure.html +++ b/docs/reference/write_faststructure.html @@ -7,7 +7,7 @@ - +
    @@ -38,7 +38,7 @@
    • - +
    @@ -91,7 +91,9 @@

    Write a faststructure file from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -100,14 +102,14 @@

    Arguments

    tidy_vcf.

    -
    plink.bed
    +

    To export in plink BED format. This will write 3 files: .bed, .bim, .fam. For this option to work, the argument data must be a GDS file or object. Default: plink.bed = FALSE.

    -
    pop.levels
    +
    pop.levels

    (optional, string) This refers to the levels in a factor. In this case, the id of the pop. Use this argument to have the pop ordered your way instead of the default @@ -117,21 +119,19 @@

    Arguments

    Default: pop.levels = NULL.

    -
    filename
    +
    filename

    (optional) The file name prefix for the faststructure file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_faststructure_.

    -
    ...
    +
    ...

    other parameters passed to the function.

    Value

    - - -

    A faststructure file is saved to the working directory.

    +

    A faststructure file is saved to the working directory.

    References

    @@ -156,15 +156,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_fineradstructure.html b/docs/reference/write_fineradstructure.html index c14859fa..7ad4aea2 100644 --- a/docs/reference/write_fineradstructure.html +++ b/docs/reference/write_fineradstructure.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,21 +83,23 @@

    Write a fineRADstructure file from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    strata
    +
    strata

    (path or object) The strata file or object. Additional documentation is available in read_strata. Use that function to whitelist/blacklist populations/individuals. Option to set pop.levels/pop.labels is also available.

    -
    filename
    +
    filename

    (optional) The file name prefix for the fineRADstructure file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_fineradstructure_.

    @@ -105,9 +107,7 @@

    Arguments

    Value

    - - -

    A fineRADstructure file is written in the working directory. +

    A fineRADstructure file is written in the working directory. An object is also returned in the global environment.

    @@ -119,7 +119,7 @@

    Details

    Life cycle

    - +

    It become increasingly difficult for me to follow all the different naming @@ -156,15 +156,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_gds.html b/docs/reference/write_gds.html index 045fc68a..c9a3ce18 100644 --- a/docs/reference/write_gds.html +++ b/docs/reference/write_gds.html @@ -7,7 +7,7 @@ - +
    @@ -38,7 +38,7 @@
    • - +
    @@ -91,20 +91,22 @@

    Write a GDS object from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    data.source
    +
    data.source

    (optional, character) The name of the software that generated the data. e.g. data.source = "Stacks v.2.4". Default: data.source = NULL.

    -
    filename
    +
    filename

    (optional) The file name of the Genomic Data Structure (GDS) file. radiator will append .gds.rad to the filename. If filename chosen is already present in the @@ -112,12 +114,12 @@

    Arguments

    Default: filename = NULL.

    -
    open
    +
    open

    (optional, logical) Open or not the radiator connection. Default: open = TRUE.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -125,9 +127,7 @@

    Arguments

    Value

    - - -

    An object in the global environment of class SeqVarGDSClass and +

    An object in the global environment of class SeqVarGDSClass and a file in the working directory.

    @@ -137,7 +137,7 @@

    References

    analysis of SNP data. Bioinformatics. 2012;28: 3326-3328. doi:10.1093/bioinformatics/bts606

    Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir BS, -Laurie C, Levine D (2017). SeqArray -- A storage-efficient high-performance +Laurie C, Levine D (2017). SeqArray – A storage-efficient high-performance data format for WGS variant calls. Bioinformatics.

    @@ -148,9 +148,9 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 data.gds <- radiator::write_gds(data = "shark.rad")
-}
+} # }
    @@ -165,15 +165,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_genepop.html b/docs/reference/write_genepop.html index bd4bdb97..f16e4249 100644 --- a/docs/reference/write_genepop.html +++ b/docs/reference/write_genepop.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -90,7 +90,9 @@

    Write a genepop file

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -99,17 +101,17 @@

    Arguments

    tidy_vcf.

    -
    pop.levels
    +
    pop.levels

    (optional, string) A character string with your populations ordered. Default: pop.levels = NULL. Described in read_strata.

    -
    genepop.header
    +
    genepop.header

    The first line of the Genepop file. Default: genepop.header = NULL will use "radiator genepop with date".

    -
    markers.line
    +
    markers.line

    (optional, logical) In the genepop and structure file, you can write the markers on a single line separated by commas markers.line = TRUE, @@ -119,21 +121,19 @@

    Arguments

    Default: markers.line = TRUE.

    -
    filename
    +
    filename

    (optional) The file name prefix for the genepop file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_genepop_.

    -
    ...
    +
    ...

    other parameters passed to the function.

    Value

    - - -

    A genepop file is saved to the working directory.

    +

    A genepop file is saved to the working directory.

    References

    @@ -165,15 +165,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_genepopedit.html b/docs/reference/write_genepopedit.html index 2c8a09e0..62b5e03a 100644 --- a/docs/reference/write_genepopedit.html +++ b/docs/reference/write_genepopedit.html @@ -18,7 +18,7 @@ - +
    @@ -49,7 +49,7 @@
    • - +
    @@ -103,7 +103,9 @@

    Write a genepopedit flatten object

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -114,9 +116,7 @@

    Arguments

    Value

    - - -

    A genepopedit object in the global environment.

    +

    A genepopedit object in the global environment.

    References

    @@ -145,15 +145,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_genind.html b/docs/reference/write_genind.html index 02d8e207..1e647e2d 100644 --- a/docs/reference/write_genind.html +++ b/docs/reference/write_genind.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Write a genind object from a tidy data frame or GDS file or object.

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -92,14 +94,14 @@

    Arguments

    tidy_vcf.

    -
    write
    +
    write

    (logical, optional) To write in the working directory the genind object. The file is written with radiator_genind_DATE@TIME.RData and can be open with load or readRDS. Default: write = FALSE.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -130,15 +132,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_genlight.html b/docs/reference/write_genlight.html index 19ef5f61..fe884a4e 100644 --- a/docs/reference/write_genlight.html +++ b/docs/reference/write_genlight.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -88,7 +88,9 @@

    Write a genlight object from a tidy data frame or GDS file or object.

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -97,20 +99,20 @@

    Arguments

    tidy_vcf.

    -
    biallelic
    +
    biallelic

    (logical, optional) If you already know that the data is biallelic use this argument to speed up the function. Default: biallelic = TRUE.

    -
    write
    +
    write

    (logical, optional) To write in the working directory the genlight object. The file is written with radiator_genlight_DATE@TIME.RData and can be open with load or readRDS. Default: write = FALSE.

    -
    dartr
    +
    dartr

    (logical, optional) For non-dartR users who wants to have a genlight object ready for the package. This option transfer or generates: CALL_RATE, AVG_COUNT_REF, AVG_COUNT_SNP, REP_AVG, @@ -120,13 +122,13 @@

    Arguments

    Default: dartr = FALSE.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    @@ -147,7 +149,7 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # With defaults:
 turtle <- radiator::write_genlight(data = "my.radiator.gds.rad")
 
@@ -161,7 +163,7 @@ 
    Examples
    
     dartr = TRUE,
     verbose = TRUE
  )
-}
+} # }
    @@ -176,15 +178,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_gsi_sim.html b/docs/reference/write_gsi_sim.html index 5760866d..6533e82b 100644 --- a/docs/reference/write_gsi_sim.html +++ b/docs/reference/write_gsi_sim.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -89,13 +89,15 @@

    Write a gsi_sim file from a data frame (wide or long/tidy).

    Arguments

    -
    data
    + + +
    data

    A tidy genomic data set in the working directory tidy formats. How to get a tidy data frame ? Look for radiator tidy_genomic_data.

    -
    pop.levels
    +
    pop.levels

    (option, string) This refers to the levels in a factor. In this case, the id of the pop. Use this argument to have the pop ordered your way instead of the default @@ -105,7 +107,7 @@

    Arguments

    strata argument that can do the same thing, see below.

    -
    pop.labels
    +
    pop.labels

    (optional, string) Use this argument to rename/relabel your pop or combine your pop. e.g. To combine "QUE" and "ONT" into a new pop called "NEW": @@ -119,7 +121,7 @@

    Arguments

    strata argument that can do the same thing, see below.

    -
    strata
    +
    strata

    (optional) A tab delimited file with 2 columns with header: INDIVIDUALS and STRATA. Default: strata = NULL. Use this argument to rename or change @@ -127,15 +129,13 @@

    Arguments

    The STRATA column can be any hierarchical grouping.

    -
    filename
    +
    filename

    The name of the file written to the working directory.

    Value

    - - -

    A gsi_sim input file is saved to the working directory.

    +

    A gsi_sim input file is saved to the working directory.

    References

    @@ -169,15 +169,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_gtypes.html b/docs/reference/write_gtypes.html index 0a92fd18..d87a2b7e 100644 --- a/docs/reference/write_gtypes.html +++ b/docs/reference/write_gtypes.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -81,7 +81,9 @@

    Write a strat

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -90,23 +92,21 @@

    Arguments

    tidy_vcf.

    -
    write
    +
    write

    (logical, optional) To write in the working directory the gtypes object. The file is written with radiator_gtypes_DATE@TIME.RData if no filename is provided and can be open with load or readRDS. Default: write = FALSE.

    -
    filename
    +
    filename

    (character, optional) Filename prefix. Default: filename = NULL.

    Value

    - - -

    An object of the class strataG is returned.

    +

    An object of the class strataG is returned.

    References

    @@ -126,14 +126,14 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # require(strataG)
 # with radiator GDS
 turtle <- radiator::write_gtypes(data = "my.radiator.gds.rad")
 
 # with tidy data
 turtle <- radiator::write_gtypes(data = "my.radiator.rad")
-}
+} # }
    @@ -148,15 +148,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_hapmap.html b/docs/reference/write_hapmap.html index fe7b5937..73028625 100644 --- a/docs/reference/write_hapmap.html +++ b/docs/reference/write_hapmap.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -81,7 +81,9 @@

    Write a HapMap file from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory.

    The data requires nucleotide A, C, G, T information for the genotypes.

    @@ -89,7 +91,7 @@

    Arguments

    Look into radiator tidy_genomic_data.

    -
    filename
    +
    filename

    (optional) The file name prefix for the hapmap file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_hapmap.

    @@ -112,15 +114,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_hierfstat.html b/docs/reference/write_hierfstat.html index d4df67f7..fb4037db 100644 --- a/docs/reference/write_hierfstat.html +++ b/docs/reference/write_hierfstat.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,14 +83,16 @@

    Write a hierfstat file from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    filename
    +
    filename

    (optional) The file name prefix for the hierfstat file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_hierfstat_.

    @@ -98,9 +100,7 @@

    Arguments

    Value

    - - -

    A hierfstat file is saved to the working directory.

    +

    A hierfstat file is saved to the working directory.

    References

    @@ -125,15 +125,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_hzar.html b/docs/reference/write_hzar.html index 4c54df56..b22aeeec 100644 --- a/docs/reference/write_hzar.html +++ b/docs/reference/write_hzar.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -88,26 +88,28 @@

    Write a HZAR file from a tidy data frame.

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    distances
    +
    distances

    (optional) A file with 2 columns, POP_ID and the distance information per populations. With default: distances = NULL, the column is left empty.

    -
    filename
    +
    filename

    (optional) The file name prefix for the HZAR file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_hzar_.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    @@ -115,9 +117,7 @@

    Arguments

    Value

    - - -

    A HZAR file is written in the working directory.

    +

    A HZAR file is written in the working directory.

    Details

    @@ -137,7 +137,7 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # The simplest form of the function:
 hzar.data <- radiator::write_hzar(data = tidydata)
 
@@ -155,7 +155,7 @@ 
    Examples
    
 # tidy the genepop file then pipe the result in write_hzar
 nanycats.hzar <- radiator::tidy_genepop(data = nancycats) %>%
     radiator::write_hzar(data = .)
-}
+} # }
    @@ -170,15 +170,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_ldna.html b/docs/reference/write_ldna.html index f5a5a518..771286c1 100644 --- a/docs/reference/write_ldna.html +++ b/docs/reference/write_ldna.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -88,7 +88,9 @@

    Write a LDna object from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? @@ -96,7 +98,7 @@

    Arguments

    The genotypes are biallelic.

    -
    filename
    +
    filename

    (optional) The file name of the LDna lower matrix file. Radiator will append .ldna.rds to the filename. If filename chosen is already present in the @@ -106,13 +108,13 @@

    Arguments

    To read the data back into R, use readRDS("filename.ldna.rds").

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    ...
    +
    ...

    (optional) To pass further argument for fine-tuning the function (see details).

    @@ -155,15 +157,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_maverick.html b/docs/reference/write_maverick.html index 68607d2c..2fee6d28 100644 --- a/docs/reference/write_maverick.html +++ b/docs/reference/write_maverick.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -81,28 +81,28 @@

    Write a maverick file from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    filename
    +
    filename

    (optional) The file name prefix for the maverick file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_maverick_.

    -
    ...
    +
    ...

    other parameters passed to the function.

    Value

    - - -

    A maverick file is saved to the working directory (with .txt).

    +

    A maverick file is saved to the working directory (with .txt).

    References

    @@ -127,15 +127,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_pcadapt.html b/docs/reference/write_pcadapt.html index e63a46fa..54213bac 100644 --- a/docs/reference/write_pcadapt.html +++ b/docs/reference/write_pcadapt.html @@ -8,7 +8,7 @@ - +
    @@ -39,7 +39,7 @@
    • - +
    @@ -93,41 +93,41 @@

    Write a p

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    pop.select
    +
    pop.select

    (optional, string) Selected list of populations for the analysis. e.g. pop.select = c("QUE", "ONT") to select QUE and ONT population samples (out of 20 pops). Default: pop.select = NULL

    -
    filename
    +
    filename

    (optional) The file name prefix for the pcadapt file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_pcadapt_.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    ...
    +
    ...

    (optional) To pass further arguments for fine-tuning the function.

    Value

    - - -

    A pcadapt file is written in the working directory a genotype matrix +

    A pcadapt file is written in the working directory a genotype matrix object is also generated in the global environment.

    @@ -139,7 +139,7 @@

    Details

    Advance mode

    - +

    dots-dots-dots ... allows to pass several arguments for fine-tuning the function:

    1. Filtering for linkage disequilibrium: 3 arguments @@ -184,15 +184,15 @@

      Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_plink.html b/docs/reference/write_plink.html index c0c921e3..d1d04b9f 100644 --- a/docs/reference/write_plink.html +++ b/docs/reference/write_plink.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,14 +83,16 @@

    Write a plink tped/tfam file from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    filename
    +
    filename

    (optional) The file name prefix for tped/tfam files written to the working directory. With default: filename = NULL, the date and time is appended to radiator_plink_.

    @@ -121,15 +123,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_rad.html b/docs/reference/write_rad.html index e6f27696..3a34acf0 100644 --- a/docs/reference/write_rad.html +++ b/docs/reference/write_rad.html @@ -14,7 +14,7 @@ - +
    @@ -45,7 +45,7 @@
    • - +
    @@ -109,45 +109,47 @@

    Write tidy genomic data file or close GDS file

    Arguments

    -
    data
    + + +
    data

    An object in the global environment: tidy data frame or GDS connection file

    -
    path
    +
    path

    (optional) For tidy data frame, the path to write the data on disk. Default: path = NULL.

    -
    filename
    +
    filename

    (optional) Name of the file (when using tsv files). Default: filename = NULL.

    -
    tsv
    +
    tsv

    (optinal, logical) To trigger saving using readr::write_tsv. Default: tsv = FALSE.

    -
    internal
    +
    internal

    (optional, logical) This is used inside radiator internal code and it stops from writting the file. Default: internal = FALSE.

    -
    append
    +
    append

    (optional, logical) If FALSE, will overwrite existing file. If TRUE, will append to existing file. In both cases, if file does not exist a new file is created. Default: append = FALSE.

    -
    col.names
    +
    col.names

    (optional, logical) Write columns names at the top of the file? Must be either TRUE or FALSE. Default: col.names = TRUE.

    -
    write.message
    +
    write.message

    (optional, character) Print a message in the console after writting file. With write.message = NULL, nothing is printed in the console. @@ -155,7 +157,7 @@

    Arguments

    message("File written: ", folder_short(filename)).

    -
    verbose
    +
    verbose

    (optional, logical) verbose = TRUE to be chatty during execution. Default: verbose = FALSE.

    @@ -163,9 +165,7 @@

    Arguments

    Value

    - - -

    A file written in the working directory or nothing if it's a GDS connection file.

    +

    A file written in the working directory or nothing if it's a GDS connection file.

    See also

    @@ -180,11 +180,11 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 require(SeqArray)
 radiator::write_rad(data = tidy.data, path = "data.shark.rad")
 radiator::write_rad(data = gds.object)
-}
+} # }
    @@ -199,15 +199,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_related.html b/docs/reference/write_related.html index 486b1833..0150ce94 100644 --- a/docs/reference/write_related.html +++ b/docs/reference/write_related.html @@ -10,7 +10,7 @@ - +
    @@ -41,7 +41,7 @@
    • - +
    @@ -96,34 +96,34 @@

    Write a related file from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    filename
    +
    filename

    (optional) The file name prefix for the related file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_related_.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    -
    ...
    +
    ...

    other parameters passed to the function.

    Value

    - - -

    A related file is saved to the working directory.

    +

    A related file is saved to the working directory.

    References

    @@ -153,15 +153,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_rubias.html b/docs/reference/write_rubias.html index 70e54123..1fb19972 100644 --- a/docs/reference/write_rubias.html +++ b/docs/reference/write_rubias.html @@ -3,7 +3,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -82,7 +82,9 @@

    Write a rubias object

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -91,7 +93,7 @@

    Arguments

    tidy_vcf.

    -
    strata
    +
    strata

    (optional, tibble file or object) This tibble of individual's metadata must contain four columns: SAMPLE_TYPE, REPUNIT, COLLECTION, INDIVIDUALS. Those columns @@ -101,14 +103,14 @@

    Arguments

    the STRATA or POP_ID column found in the data.

    -
    filename
    +
    filename

    The prefix for the name of the file written to the working directory. Default: filename = NULL. With default, only the rubias object is generated. The filename will be appended _rubias.tsv.

    -
    parallel.core
    +
    parallel.core

    (optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

    @@ -116,9 +118,7 @@

    Arguments

    Value

    - - -

    A rubias object in the global environment and a file is written in the +

    A rubias object in the global environment and a file is written in the working directory if filename argument was used.

    @@ -155,15 +155,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_snprelate.html b/docs/reference/write_snprelate.html index cabf6579..aec57f5b 100644 --- a/docs/reference/write_snprelate.html +++ b/docs/reference/write_snprelate.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Write a SNPRelate object from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? @@ -91,13 +93,13 @@

    Arguments

    The genotypes are biallelic.

    -
    biallelic
    +
    biallelic

    (logical, optional) If you already know that the data is biallelic use this argument to speed up the function. Default: biallelic = TRUE.

    -
    filename
    +
    filename

    (optional) The file name of the Genomic Data Structure (GDS) file. radiator will append .gds to the filename. If filename chosen is already present in the @@ -105,7 +107,7 @@

    Arguments

    Default: filename = NULL.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -113,9 +115,7 @@

    Arguments

    Value

    - - -

    An object in the global environment of class +

    An object in the global environment of class "SNPGDSFileClass", "gds.class" and a file in the working directory.

    @@ -137,10 +137,10 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 require(SNPRelate)
 data.gds <- radiator::write_snprelate(data = "shark.rad")
-}
+} # }
    @@ -155,15 +155,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_stockr.html b/docs/reference/write_stockr.html index 2a4365cf..58e48140 100644 --- a/docs/reference/write_stockr.html +++ b/docs/reference/write_stockr.html @@ -5,7 +5,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +
    @@ -81,7 +81,9 @@

    Write a stockR dataset from a tidy data frame or GDS file or object.

    Arguments

    -
    data
    + + +
    data

    (4 options) A file or object generated by radiator:

    • tidy data

    • Genomic Data Structure (GDS)

    How to get GDS and tidy data ? @@ -90,14 +92,14 @@

    Arguments

    tidy_vcf.

    -
    filename
    +
    filename

    (optional) The stockr object is written in the working directory. The file is written with radiator_stockr_DATE@TIME.RData and can be open with readRDS. Default: filename = NULL.

    -
    verbose
    +
    verbose

    (optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

    @@ -105,9 +107,7 @@

    Arguments

    Value

    - - -

    The object generated is a matrix with +

    The object generated is a matrix with dimension: MARKERS x INDIVIDUALS. The genotypes are coded like PLINK: 0, 1 or 2 alternate allele. 0: homozygote for the reference allele, 1: heterozygote, 2: homozygote for the alternate allele. @@ -137,15 +137,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_structure.html b/docs/reference/write_structure.html index bbe38255..a9143895 100644 --- a/docs/reference/write_structure.html +++ b/docs/reference/write_structure.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -83,14 +83,16 @@

    Write a structure file from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    pop.levels
    +
    pop.levels

    (optional, string) This refers to the levels in a factor. In this case, the id of the pop. Use this argument to have the pop ordered your way instead of the default @@ -100,21 +102,19 @@

    Arguments

    Default: pop.levels = NULL.

    -
    filename
    +
    filename

    (optional) The file name prefix for the structure file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_structure_.

    -
    ...
    +
    ...

    other parameters passed to the function.

    Value

    - - -

    A structure file is saved to the working directory.

    +

    A structure file is saved to the working directory.

    References

    @@ -139,15 +139,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/write_vcf.html b/docs/reference/write_vcf.html index 8b5c4cdb..918b1b1a 100644 --- a/docs/reference/write_vcf.html +++ b/docs/reference/write_vcf.html @@ -6,7 +6,7 @@ - +
    @@ -37,7 +37,7 @@
    • - +
    @@ -89,14 +89,16 @@

    Write a vcf file from a tidy data frame

    Arguments

    -
    data
    + + +
    data

    A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.

    -
    pop.info
    +
    pop.info

    (optional, logical) Should the population information be included in the FORMAT field (along the GT info for each samples ?). To make the VCF population-ready use pop.info = TRUE. The population information @@ -104,17 +106,17 @@

    Arguments

    Default: pop.info = FALSE. Experimental.

    -
    filename
    +
    filename

    (optional) The file name prefix for the vcf file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_vcf_file_.

    -
    source
    +
    source

    source of vcf

    -
    empty
    +
    empty

    generate an empty vcf

    @@ -149,15 +151,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/vignettes/rad_genomics_computer_setup.Rmd b/vignettes/rad_genomics_computer_setup.Rmd index 5d659e76..f86b5ef4 100644 --- a/vignettes/rad_genomics_computer_setup.Rmd +++ b/vignettes/rad_genomics_computer_setup.Rmd @@ -57,7 +57,7 @@ In this vignette I present *brewless* options only. ## Update your OS -* the current version is macOS Ventura 13.0 +* the current version is macOS Sequoia 15.1 * [how to update](http://support.apple.com/kb/HT1338?viewlocale=en_US&locale=en_US) @@ -116,34 +116,34 @@ The command below fro both GCC and Clang will: Choose the binary version number based on your OS and change the version accordingly [link](http://hpc.sourceforge.net). -**Ventura and Monterey** [gcc-11.2-bin.tar.gz](http://prdownloads.sourceforge.net/hpc/gcc-11.2-bin.tar.gz) +**Sonoma** [gcc-14.1-m1-bin.tar.gz](http://prdownloads.sourceforge.net/hpc/gcc-14.1-m1-bin.tar.gz) ```{bash eval=FALSE} #In Terminal cd Downloads -sudo tar -zxvf gcc-11.2-bin.tar.gz -C /usr/local --strip-components=2 +sudo tar -zxvf gcc-14.1-m1-bin.tar.gz -C /usr/local --strip-components=2 ``` ```{bash eval=FALSE} -sudo rm gcc-11.2-bin.tar.gz +sudo rm gcc-14.1-m1-bin.tar.gz gcc -v ``` ### Update Clang -We want [clang](https://en.wikipedia.org/wiki/Clang) compiler with OpenMP enabled. The latest version is [15.0.3](https://github.com/llvm/llvm-project/releases/tag/llvmorg-15.0.3). +We want [clang](https://en.wikipedia.org/wiki/Clang) compiler with OpenMP enabled. The latest version is [19.1.3](https://github.com/llvm/llvm-project/releases/tag/llvmorg-19.1.3). ```{bash eval=FALSE} -#In browser -https://github.com/llvm/llvm-project/releases/download/llvmorg-15.0.3/clang+llvm-15.0.3-x86_64-apple-darwin.tar.xz +#In browser make sure you know if your mac as an Intel or Mac chips (M1, M2, etc) +https://github.com/llvm/llvm-project/releases/download/llvmorg-19.1.3/LLVM-19.1.3-macOS-X64.tar.xz #In Terminal cd Downloads -sudo tar -xzvf clang+llvm-15.0.3-x86_64-apple-darwin.tar.xz -C/usr/local --strip-components=1 +sudo tar -xzvf LLVM-19.1.3-macOS-X64.tar.xz -C/usr/local --strip-components=1 ``` ```{bash eval=FALSE} -sudo rm clang+llvm-15.0.3-x86_64-apple-darwin.tar.xz +sudo rm LLVM-19.1.3-macOS-X64.tar.xz clang -v ``` @@ -237,13 +237,12 @@ Several flavors available, check for the proper [link](http://releases.llvm.org/ # Install [R](https://cran.r-project.org) - -To install R v4.2.1 **"Funny-Looking Kid"** released on 2022-06-23 download the +To install R v4.4.2 **"Pile of Leaves"** released on 2024-10-31 download the installer and follow the instructions ```{bash eval=FALSE} # for macOS cd Downloads -curl -O https://cran.r-project.org/bin/macosx/R-4.2.1.pkg +curl -O https://cran.r-project.org/bin/macosx/R-4.4.2.pkg ``` @@ -722,7 +721,7 @@ terminal [zstd](https://facebook.github.io/zstd/) and [lz4](https://lz4.github.i ```{bash eval=FALSE} cd ~/Downloads -curl -L https://github.com/lz4/lz4/archive/refs/tags/v1.9.4.tar.gz | tar xf - +curl -L https://github.com/lz4/lz4/archive/refs/tags/v1.10.0.tar.gz | tar xf - cd lz4* make sudo make install @@ -732,7 +731,7 @@ sudo rm -R lz4* ```{bash eval=FALSE} cd ~/Downloads -curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.5.tar.gz | tar xf - +curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.6.tar.gz | tar xf - cd zstd* make sudo make install diff --git a/vignettes/rad_genomics_computer_setup.html b/vignettes/rad_genomics_computer_setup.html index a5be6772..25056781 100644 --- a/vignettes/rad_genomics_computer_setup.html +++ b/vignettes/rad_genomics_computer_setup.html @@ -10,7 +10,7 @@ - + RADseq Genomics in R @@ -1480,7 +1480,7 @@

    RADseq Genomics in R

    computer setup

    -

    2024-04-30

    +

    2024-11-06

    @@ -1523,7 +1523,7 @@

    macOS

    Update your OS

      -
    • the current version is macOS Ventura 13.0
      • +
    • the current version is macOS Sequoia 15.1
    • how to update
    @@ -1584,23 +1584,23 @@

    Compiler

    Update GCC

    Choose the binary version number based on your OS and change the version accordingly link.

    -

    Ventura and Monterey gcc-11.2-bin.tar.gz

    +

    Sonoma gcc-14.1-m1-bin.tar.gz

    #In Terminal
 cd Downloads
-sudo tar -zxvf gcc-11.2-bin.tar.gz -C /usr/local --strip-components=2
    -
    sudo rm gcc-11.2-bin.tar.gz
+sudo tar -zxvf gcc-14.1-m1-bin.tar.gz -C /usr/local --strip-components=2
    +
    sudo rm gcc-14.1-m1-bin.tar.gz
 gcc -v

    Update Clang

    We want clang -compiler with OpenMP enabled. The latest version is 15.0.3.

    -
    #In browser
-https://github.com/llvm/llvm-project/releases/download/llvmorg-15.0.3/clang+llvm-15.0.3-x86_64-apple-darwin.tar.xz
+compiler with OpenMP enabled. The latest version is 19.1.3.
    
+
    #In browser make sure you know if your mac as an Intel or Mac chips (M1, M2, etc)
+https://github.com/llvm/llvm-project/releases/download/llvmorg-19.1.3/LLVM-19.1.3-macOS-X64.tar.xz
 #In Terminal
 cd Downloads
-sudo tar -xzvf clang+llvm-15.0.3-x86_64-apple-darwin.tar.xz -C/usr/local --strip-components=1
    
-
    sudo rm clang+llvm-15.0.3-x86_64-apple-darwin.tar.xz
+sudo tar -xzvf LLVM-19.1.3-macOS-X64.tar.xz -C/usr/local --strip-components=1
    
+
    sudo rm LLVM-19.1.3-macOS-X64.tar.xz
 clang -v
    @@ -1669,11 +1669,11 @@

    Linux

    Install R

    -

    To install R v4.2.1 “Funny-Looking Kid” released on -2022-06-23 download the installer and follow the instructions

    +

    To install R v4.4.2 “Pile of Leaves” released on +2024-10-31 download the installer and follow the instructions

    # for macOS
 cd Downloads
-curl -O https://cran.r-project.org/bin/macosx/R-4.2.1.pkg
    +curl -O https://cran.r-project.org/bin/macosx/R-4.4.2.pkg

    To remove R completely from macOS

    sudo rm -rf /Library/Frameworks/R.framework /Applications/R.app \
 /usr/bin/R /usr/bin/Rscript
    @@ -2055,14 +2055,14 @@

    fst & fstcore &

    Better to install and compile them from source to enable OpenMP. Install in the terminal zstd and lz4:

    cd ~/Downloads
-curl -L https://github.com/lz4/lz4/archive/refs/tags/v1.9.4.tar.gz | tar xf -
+curl -L https://github.com/lz4/lz4/archive/refs/tags/v1.10.0.tar.gz | tar xf -
 cd lz4*
 make 
 sudo make install
 cd .. 
 sudo rm -R lz4*
    cd ~/Downloads
-curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.5.tar.gz | tar xf -
+curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.6.tar.gz | tar xf -
 cd zstd*
 make 
 sudo make install
@@ -2408,7 +2408,7 @@ 
    macOS Terminal from specific folder
    
 Terminal Tab at Folder. Now you can right-click your track pad
 or mouse on a folder and choose Services -> New Terminal at
 Folder!
    
-
    
+

    Shortcut to folder path

    @@ -2420,7 +2420,7 @@

    Shortcut to folder path

    Middle, choose: Copy to Clipboard and drag it to the right panel Now you want to have: Service receives selected FILES OR FOLDERS in FINDER> You should have something similar to the image below:     -

    +

    Save (cmd-S) or File -> Save service as: copy path to clipboard

    Go in the Finder, select a folder and right click on it you should see ‘copy path to clipboard’ at the bottom or in