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.
- 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)
Analyses are organized in numerical order under the ./src directory.
Results are stored in a Dryad repository: https://doi.org/10.5061/dryad.w3r2280nw
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