Performs over‐representation testing via DOSE/clusterProfiler against KEGG or custom gene sets.
Usage
pathway_enrich(
gene,
organism = "ppu",
keyType = "kegg",
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
universe,
minGSSize = 10,
maxGSSize = 500,
qvalueCutoff = 0.2,
use_internal_kegg = FALSE,
custom_gene_sets = FALSE,
custom_pathways = NULL
)Arguments
- gene
Character vector of gene or protein IDs to test for enrichment.
- organism
KEGG organism code (e.g.
"ppu").- keyType
ID type (default
"kegg").- pvalueCutoff
Numeric; p‐value cutoff (default
0.05).- pAdjustMethod
Character; adjustment method (default
"BH").- universe
Character vector of background IDs.
- minGSSize
Integer; minimum gene set size.
- maxGSSize
Integer; maximum gene set size.
- qvalueCutoff
Numeric; q‐value cutoff (default
0.2).- use_internal_kegg
Logical; use internal KEGG DB if
TRUE.- custom_gene_sets
Logical; use custom gene sets if
TRUE.- custom_pathways
Data frame with columns
"Pathway"and"Accession", or a GMT file path.