getKeggGeneSetDb: Retrieves a GeneSetDb from KEGG's REST API

In lianos/multiGSEA: A unified interface to a plethora of gene set enrichment analysis methods

Description

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

Usage

getKeggGeneSetDb(
  species = "human",
  id.type = c("ensembl", "entrez"),
  database = "pathway",
  idxref = NULL,
  ...
)

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 remap_identifiers(). If speciesis not "human" or "mouse", you need to provide an idxref table that works with remap_identifiers().

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.

Value

A GeneSetDb of the kegg stuffs

Examples

## Not run: 
mouse.entrez <- getKeggGeneSetDb("mouse")
mouse.ens <- getKeggGeneSetDb("mouse", id.type = "ensembl")

## End(Not run)

lianos/multiGSEA documentation built on Nov. 17, 2020, 1:26 p.m.