Get geneset collection

Usage

get_geneset(
  geneset,
  source = c("auto", "builtin", "list", "gmt", "data.frame", "msigdb", "go", "kegg",
    "reactome", "wikipathways", "biocarta"),
  species = "Homo sapiens",
  collection = "H",
  subcollection = NULL,
  ontology = c("BP", "MF", "CC"),
  version = NA_character_
)

Arguments

geneset: Geneset input.
source: Geneset source. One of auto, builtin, list, gmt, data.frame, msigdb, go, kegg, reactome, wikipathways, biocarta.
species: Species label used by external geneset sources.
collection: MSigDB collection (for source = msigdb).
subcollection: MSigDB subcollection (for source = msigdb).
ontology: GO ontology (BP, MF, CC) for source = go.
version: Optional source version string.

Value

Named list of pathways to genes with source metadata attached.