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Run Gene Set Enrichment Analysis

Source: R/gsea_functions.R
run_gsea.Rd

This function performs Gene Set Enrichment Analysis (GSEA) using clusterProfiler to identify enriched gene sets in the differential expression results. It can use either pre-defined MSigDB gene sets or custom gene sets.

Usage

run_gsea(
  res,
  org,
  msigdbr = import_msigdbr(org),
  save_data = T,
  save_dir = getwd()
)

Arguments

res

Differential expression result data frame from run_diffexp()

org

The organism to use, either "human" or "mouse".

save_data

Logical. If TRUE, saves results to TSV and RDS files. Default is TRUE

save_dir

Directory to save the results. Default is current working directory

custom_msigdb

Dataframe or path to a custom gene set database in GMT format. Default is NULL

Value

A list of GSEA results for each gene set collection, with each element containing: - gene set name - normalized enrichment score (NES) - p-value and adjusted p-value - leading edge genes - collection name - comparison name

Examples

if (FALSE) { # \dontrun{
# Run GSEA with default MSigDB gene sets
gsea_results <- run_gsea(res)

# Run GSEA with custom gene sets
gsea_results <- run_gsea(res, custom_msigdb = "path/to/custom_sets.tsv")

# Run GSEA for mouse data
gsea_results <- run_gsea(res, org = "mouse")
} # }