Run KEGG enrichment directly from a VISTA comparison

Usage

get_kegg_enrichment(
  x,
  sample_comparison,
  regulation = c("Up", "Down", "Both", "All"),
  from_type = "SYMBOL",
  orgdb = NULL,
  species = "Mus musculus",
  kegg_species = NULL,
  background = NULL,
  ...
)

Arguments

x: A VISTA object with DE results.
sample_comparison: Comparison name to use.
regulation: One of "Up", "Down", "Both", or "All"; selects genes.
from_type: Identifier type in the DE tables (default "SYMBOL").
orgdb: OrgDb object; defaults to mouse/human based on species.
species: Species name to infer default OrgDb.
kegg_species: KEGG organism code (e.g., "mmu" or "hsa"). If NULL, inferred from species.
background: Optional background gene set; default uses all features.
...: Passed to clusterProfiler::enrichGO().

Value

An object returned by this function.

Examples

v <- example_vista()
comp <- names(comparisons(v))[1]
if (requireNamespace('org.Mm.eg.db', quietly = TRUE)) {
  out <- try(get_kegg_enrichment(v, sample_comparison = comp, from_type = 'ENSEMBL', orgdb = org.Mm.eg.db::org.Mm.eg.db), silent = TRUE)
  if (!inherits(out, 'try-error')) out
}