Run GSEA wrapper — run_gsea_wrapper • deseq2pip

This function runs GSEA for all comparisons and collections.

Usage

run_gsea_wrapper(
  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.

Value

A list of GSEA results for each gene set collection

Examples

if (FALSE) { # \dontrun{
# Run GSEA wrapper
gsea_results <- run_gsea_wrapper(res)
} # }