Run GSEA (Gene Set Enrichment Analysis) — run

Performs GO or KEGG GSEA using ranked gene statistics. This function dynamically loads clusterProfiler and annotation packages only when needed, making them optional dependencies.

Usage

run_gsea(
  df,
  gene_col = "gene",
  stat_col = "log2FC",
  db = c("GO", "KEGG"),
  ont = "ALL",
  species = c("human", "mouse"),
  keyType = "SYMBOL",
  qvalue_cutoff = 0.05,
  minGSSize = 10,
  maxGSSize = 5000,
  pAdjustMethod = "BH",
  eps = 1e-10,
  use_internal_data = FALSE,
  seed = 123
)

Arguments

df: A data frame containing ranking statistics and gene IDs.
gene_col: Column storing gene IDs.
stat_col: Column storing ranking values (e.g. log2FC).
db: Database for GSEA: "GO" or "KEGG".
ont: GO ontology ("BP","CC","MF","ALL").
species: Species: "human" or "mouse".
keyType: Gene ID type (default SYMBOL).
qvalue_cutoff: Q-value filter.
minGSSize: Minimum gene set size.
maxGSSize: Maximum gene set size.
pAdjustMethod: Multiple testing correction.
eps: GSEA numeric convergence threshold.
use_internal_data: whether using internal KEGG data
seed: Random seed.

Value

A gseaResult object.