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]