getKegg {phenoTest}R Documentation

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

Description

This function creates a list of gene sets based on KEGG 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 KeggGeneSets from package HTSanalyzeR.

Usage

getKegg(species = "Dm")

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")).

Details

This function relies on the following packages: GSEABase, KEGG.db.

Value

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

Author(s)

Evarist Planet.

See Also

getGo

Examples

#library(KEGG.db)
#library(org.Hs.eg.db)
#kegg.Hs <- getKegg('Hs')
#str(kegg.Hs)
#kegg.Hs[1:2]
[Package phenoTest version 1.28.0 Index]