Load Gene Ontology genesets

Usage

get_GeneOntology(
  onto = c("BP", "MF", "CC"),
  to = "ENSEMBL",
  includeOffspring = TRUE,
  org = "hsa"
)

Arguments

onto: array of categories to load
to: convert gene names to this type using EnrichmentBrowser::idMap(). See EnrichmentBrowser::idTypes(org="hsa") for valid types
includeOffspring: if TRUE, follow the GO hierarchy down and include all genes in offspring sets for a given gene set
org: organism. human ('hsa'), mouse ('mmu'), etc

Value

Gene sets stored as GeneSetCollection

Details

This function loads the GO gene sets using the packages EnrichmentBrowser and GO.db It can take a mintute to load because converting gene name type is slow.

Examples

# load GO Biological Process
# gs = get_GeneOntology('BP')

# load all gene sets
# gs = get_GeneOntology()