get.kegg.genesets {EnrichmentBrowser}R Documentation

Definition of gene sets according to KEGG pathways for a specified organism

Description

This function retrieves KEGG gene sets for an organism under investigation either via download from the KEGG REST server.

Usage

    get.kegg.genesets( pwys, cache = TRUE, gmt.file = NULL )

Arguments

pwys

Either a list of KEGGPathway objects or an absolute file path of a zip compressed archive of pathway xml files in KGML format. Alternatively, an organism in KEGG three letter code, e.g. ‘hsa’ for ‘Homo sapiens’.

cache

Logical. Should a locally cached version used if available? Defaults to TRUE.

gmt.file

Gene set file in GMT format. See details.

Details

The GMT (Gene Matrix Transposed) file format is a tab delimited file format that describes gene sets. In the GMT format, each row represents a gene set. Each gene set is described by a name, a description, and the genes in the gene set. See references.

Value

A list of gene sets (vectors of gene IDs).

Author(s)

Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>

References

GMT file format http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats

KEGG Organism code http://www.genome.jp/kegg/catalog/org_list.html

See Also

keggList, keggLink, KEGGPathway-class, parseKGML

Examples

    # WAYS TO DEFINE GENE SETS ACCORDING TO HUMAN KEGG PATHWAYS

    # (1) from scratch: via organism ID 
    
    gs <- get.kegg.genesets("hsa")
    

    # (2) extract from pathways
    # download human pathways via: 
    # pwys <- download.kegg.pathways("hsa")
    pwys <- system.file("extdata/hsa_kegg_pwys.zip", package="EnrichmentBrowser")
    gs <- get.kegg.genesets(pwys)

[Package EnrichmentBrowser version 2.8.7 Index]