get.kegg.genesets {EnrichmentBrowser} | R Documentation |
This function retrieves KEGG gene sets for an organism under investigation either via download from the KEGG REST server.
get.kegg.genesets( pwys, cache = TRUE, gmt.file = NULL )
pwys |
Either a list of |
cache |
Logical.
Should a locally cached version used if available?
Defaults to |
gmt.file |
Gene set file in GMT format. See 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.
A list of gene sets (vectors of gene IDs).
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
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
keggList
, keggLink
,
KEGGPathway-class
,
parseKGML
# 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)