Functional enrichment analysis (GO / KEGG) — enrichment

This function performs GO or KEGG enrichment analysis using clusterProfiler. Dependencies are loaded dynamically via requireNamespace(), so the function will only require clusterProfiler and annotation packages when executed.

Usage

enrichment_analysis(
  gene,
  db = c("GO", "KEGG"),
  species = c("human", "mouse"),
  keyType = "SYMBOL",
  qvalue_cutoff = 0.05,
  use_internal_data = TRUE,
  return_data = TRUE
)

Arguments

gene: A character vector of gene symbols.
db: Database to use: "GO" or "KEGG".
species: Species: "human" or "mouse".
keyType: Gene ID type used in gene, e.g. "SYMBOL".
qvalue_cutoff: Q-value threshold for filtering.
use_internal_data: whether using internal KEGG data
return_data: Logical. If TRUE, return enriched@result; otherwise return the full enrichment result object.

Value

A data frame or enrichment result object.

Details

KEGG analysis automatically converts gene IDs to ENTREZID using clusterProfiler::bitr(). Human and mouse annotation packages (org.Hs.eg.db and org.Mm.eg.db) are used depending on species.

Examples

if (FALSE) { # \dontrun{
enrichment_analysis(c("TP53","MDM2"), db="GO", species="human")
} # }