GOGeneSets: Create a list of gene sets based on GO terms

In HTSanalyzeR: Gene set over-representation, enrichment and network analyses for high-throughput screens

Description

This function creates a list of gene sets based on GO terms. It is species-specific, and returns a list of gene sets, each of which is a character vector of Entrez identifiers.

Usage

GOGeneSets(species = "Dm", ontologies = "MF")

Arguments

species	a single character value specifying a choice of species: "Dm" ("Drosophila_ melanogaster"), "Hs" ("Homo_sapiens"), "Rn" ("Rattus_norvegicus"), "Mm" ("Mus_musculus") or "Ce" ("Caenorhabditis_elegans"))
ontologies	a single character value or a character vector specifying an ontology or multiple ontologies. The current version provides the following choices: "BP", "CC" and "MF"

Details

This function relies on the following packages: GSEABase, GO.db, and either org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ce.eg.db, org.Dm.eg.db.

Value

a list of gene sets, with names as GO IDs. Each gene set is a character vector of Entrez identifiers.

Author(s)

Camille Terfve

See Also

KeggGeneSets

Examples

library(GO.db)
library(org.Dm.eg.db)
Dm_GO_CC<-GOGeneSets(species="Dm",ontologies=c("CC"))

HTSanalyzeR documentation built on Oct. 31, 2019, 7:10 a.m.