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