This function runs the GSEA pipeline for all comparisons and collections.
Usage
run_gsea_pip(
res,
org,
msigdbr = import_msigdbr(org),
save_data = T,
group_save_dir
)Arguments
- res
Differential expression result data frame from run_diffexp()
- org
The organism to use, either "human" or "mouse".
- msigdbr
Dataframe or path to a custom gene set database in GMT format. Default is NULL
- save_data
Logical. If TRUE, saves results to RDS and TSV files. Default is TRUE
- group_save_dir
Directory to save the results.