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sage-lungfunction

Analysis and plotting code for analyses of lung function in the Study of African Americans, Asthma, Genes, and Enviornments (SAGE). Nota Bene: this code is provided as a template, an example, and a receipt, but it is not designed as a batteries-included workflow. Interested users will need to configure several file paths to make this code useable.

Prerequisites

  • R version >= 3.5
  • PAINTOR v3.0
  • Python 2.7 (no Python 3 code used here)

The R/Bioconductor packages used here are:

  • GENESIS
  • GWASTools
  • RColorBrewer
  • SNPRelate
  • arsenal
  • coda
  • corrplot
  • data.table
  • doParallel
  • gdsfmt
  • ggcorrplot
  • ggrepel
  • grid
  • gridExtra
  • methods
  • optparse
  • tidyverse (ggplot2, dplyr, tidyr, readr, purrr, tibble, stringr, forcats)

Code

Analyses are organized in numerical order under the ./src directory.

Results

Results are stored in a Dryad repository: https://doi.org/10.5061/dryad.w3r2280nw

Preprint

If you wish to refer to these project, then please cite our preprint on bioRxiv:

Goddard PC, Keys KL, White MJ, et al. (2020) ''Integrative genomic analysis in African American children with asthma finds 3 novel loci associated with lung function''. https://doi.org/10.1101/2020.05.01.045468