Retrieves the KEGG gene set collection via its REST API

Source: R/get-kegg.R

Uses limma::getGeneKEGGLinks() and limma::getKEGGPathwayNames() internally.

getKeggCollection(species = "human", id.type = c("ensembl", "entrez"), ...)

getKeggGeneSetDb(species = "human", id.type = c("ensembl", "entrez"), ...)

Arguments

species

"human", "mouse" or any of the bioconductor or kegg-style abbreviations.

id.type

Gene identifiers are returned by the REST service as entrez identifiers. Set this to "ensembl" to translate them internally using convertIdentifiers(). If speciesis not "human" or "mouse", you need to provide an idxref table that works with convertIdentifiers().

...

pass through arguments

Value

A BiocSet of the kegg stuffs

Details

Currently we just support the pathway database, and only entrez ids.

Note that it is your responsibility to ensure that you can use the KEGG database according to their licensing requirements.

Functions

  • getKeggGeneSetDb(): method that returns a GeneSetDb

Examples

# \donttest{
# connects to the internet and takes a while
mouse.entrez <- getKeggCollection("mouse", id.type = "entrez")
human.enrez <- getKeggCollection("human", id.type = "entrez")
# }