fix links NOTEs for CRAN

DESCRIPTION

@@ -2,8 +2,8 @@ Encoding: UTF-8
 Package: bigsnpr
 Type: Package
 Title: Analysis of Massive SNP Arrays
-Version: 1.12.14
-Date: 2024-09-10
+Version: 1.12.15
+Date: 2024-09-20
 Authors@R: c(
     person("Florian", "Privé", email = "[email protected]", role = c("aut", "cre")),
     person("Michael", "Blum", role = "ths"),

R/apply-parallelize.R

@@ -10,10 +10,10 @@
 #'
 #' @inheritParams bigsnpr-package
 #' @param FUN The function to be applied. It must take a
-#' [FBM.code256][FBM.code256-class] as first argument and `ind.chr`,
+#' [FBM.code256][bigstatsr::FBM.code256-class] as first argument and `ind.chr`,
 #' an another argument to provide subsetting over SNPs.
 #' You can access the number of the chromosome by using `attr(ind.chr, "chr")`.
-#' @param combine function that is used by [foreach] to process the tasks
+#' @param combine function that is used by [foreach::foreach] to process the tasks
 #' results as they generated. This can be specified as either a function or a
 #' non-empty character string naming the function. Specifying 'c' is useful
 #' for concatenating the results into a vector, for example. The values 'cbind'

R/bigSNP-class.R

@@ -19,7 +19,7 @@ CODE_DOSAGE <- c(0, 1, 2, NA, 0, 1, 2, seq(0, 2, by = 0.01), rep(NA, 48))
 #' An S3 class for representing information on massive SNP arrays.
 #'
 #' @return A named list with at least 3 slots: \describe{
-#'   \item{genotypes}{A [FBM.code256][FBM.code256-class] which is
+#'   \item{genotypes}{A [FBM.code256][bigstatsr::FBM.code256-class] which is
 #'     a special Filebacked Big Matrix encoded with type `raw` (one byte
 #'     unsigned integer), representing genotype calls and possibly imputed
 #'     allele dosages. Rows are individuals and columns are SNPs.}

R/external-software.R

@@ -601,7 +601,7 @@ snp_plinkKINGQC <- function(plink2.path,
 #' @param plink.options Other options to be passed to PLINK as a string. More
 #'   options can be found at \url{https://www.cog-genomics.org/plink2/filter}.
 #' @param ncores Number of cores used. Default doesn't use parallelism.
-#'   You may use [nb_cores].
+#'   You may use [bigstatsr::nb_cores()].
 #'
 #' @references Browning, Brian L., and Sharon R. Browning.
 #' "Genotype imputation with millions of reference samples."

R/ldsc.R

@@ -173,7 +173,6 @@ snp_ldsc <- function(ld_score, ld_size, chi2, sample_size,
 #'     when using a mixed model, the effective sample size needs to be adjusted
 #'     as well, see \doi{10.1016/j.xhgg.2022.100136}.
 #' @param ind.beta Indices in `corr` corresponding to `df_beta`. Default is all.
-#' @inheritDotParams snp_ldsc chi2_thr1 chi2_thr2
 #'
 #' @export
 #'
@@ -195,7 +194,8 @@ snp_ldsc2 <- function(corr, df_beta,
                       intercept = 1,
                       ncores = 1,
                       ind.beta = cols_along(corr),
-                      ...) {
+                      chi2_thr1 = 30,
+                      chi2_thr2 = Inf) {
 
   assert_df_with_names(df_beta, c("beta", "beta_se", "n_eff"))
   assert_lengths(ind.beta, rows_along(df_beta))
@@ -218,7 +218,8 @@ snp_ldsc2 <- function(corr, df_beta,
     blocks      = blocks,
     intercept   = intercept,
     ncores      = ncores,
-    ...
+    chi2_thr1   = chi2_thr1,
+    chi2_thr2   = chi2_thr2
   )
 }
 

R/modify-positions.R

@@ -163,16 +163,19 @@ snp_asGeneticPos <- function(infos.chr, infos.pos, dir = tempdir(), ncores = 1,
 
 #' Download a genetic map
 #'
-#' @param type Which genetic map to download. The hg19 ones are downloaded from
-#' \url{https://github.com/joepickrell/1000-genomes-genetic-maps/} while the
-#' hg38 is downloaded from
-#' \url{https://alkesgroup.broadinstitute.org/Eagle/downloads/tables/}.
+#' @param type Which genetic map to download.
 #' @param dir Directory where to download and decompress files.
 #' @inheritParams bigsnpr-package
 #'
 #' @return A data frame with 3 columns: `chr`, `pos`, and `pos_cM`.
 #' @export
 #'
+#' @details
+#' The hg19 genetic maps are downloaded from
+#' \url{https://github.com/joepickrell/1000-genomes-genetic-maps/}
+#' while the hg38 one is downloaded from
+#' `https://alkesgroup.broadinstitute.org/Eagle/downloads/tables/`.
+#'
 #' @rdname snp_asGeneticPos2
 #'
 download_genetic_map <- function(type = c("hg19_OMNI", "hg19_hapmap", "hg38_price"),

R/read-bgen.R

@@ -122,7 +122,7 @@ check_bgen_format <- function(bgenfile) {
 #'   file, and use e.g. `match()` to get indices corresponding to the ones you want.
 #'
 #' @param ncores Number of cores used. Default doesn't use parallelism.
-#'   You may use [nb_cores()].
+#'   You may use [bigstatsr::nb_cores()].
 #' @param read_as How to read BGEN probabilities? Currently implemented:
 #'   - as dosages (rounded to two decimal places), the default,
 #'   - as hard calls, randomly sampled based on those probabilities