R: Create a list of gene sets based on GO pathways terms.

getGo {phenoTest}

R Documentation

Create a list of gene sets based on GO pathways terms.

Description

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

This function is a wraper to the function GOGeneSets from

Usage

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

Arguments

`species`	a single character value specifying the 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.

Value

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

Author(s)

Evarist Planet.

Examples

#library(GO.db)
#library(org.Hs.eg.db)
#go.Hs <- getGo('Hs')
#str(go.Hs)
#go.Hs[1:2]

[Package phenoTest version 1.28.0 Index]