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Perform KEGG Gene Set Enrichment Analysis (GSEA)

gse_kegg.Rd

A wrapper around clusterProfiler::gseKEGG to perform GSEA on a ranked list of genes and convert IDs to readable gene symbols.

Usage

gse_kegg(
  gene_list,
  enrich_pvalue = 1,
  org = org.Hs.eg.db::org.Hs.eg.db,
  organism = "hsa"
)

Arguments

gene_list

A named numeric vector of genes. Names should be Entrez IDs and values should be the ranking metric (e.g., log2 fold change).

enrich_pvalue

The p-value cutoff for enrichment. Defaults to 1 (no cutoff).

org

An organism annotation database (e.g., org.Hs.eg.db) used to map Entrez IDs to gene symbols.

organism

A character string for the KEGG organism code (e.g., 'hsa' for human).

Value

A gseKEGGResult object if the analysis is successful and finds enriched pathways, otherwise NULL.