get_GeneOntology: Load Gene Ontology genesets

In GabrielHoffman/zenith: Gene set analysis following differential expression using linear (mixed) modeling with dream

Load Gene Ontology genesets

Description

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

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.

Value

Gene sets stored as GeneSetCollection

Examples

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

# load all gene sets
# gs = get_GeneOntology()

GabrielHoffman/zenith documentation built on March 10, 2024, 11:43 p.m.