fetchAnnotation: Fetch ENSEMBL ids, ENTREZ ids and gene names using bioMart

In sansomlab/gsfisher: Geneset Fisher

Fetch ENSEMBL ids, ENTREZ ids and gene names using bioMart

Description

Fetches annotations for human ("hs") or mouse ("mm") from the Ensembl BioMart.

Usage

fetchAnnotation(
  species = c("hs", "mm"),
  ensembl_version = NULL,
  ensembl_host = NULL
)

Arguments

species	Species identifier (only "hs" or "mm" are supported).
ensembl_version	Version of the ensembl annotation to use, passed to biomaRt::useEnsembl. The default NULL uses the current annotation release.
ensembl_host	The address of the ensembl host The default NULL uses www.ensembl.org

Details

Only human "hs" and mouse "mm" are supported. Annotation must contain the columns "entrez_id" and "gene_name".

Value

A data.frame of three columns: c("ensembl_id", "entrez_id", "gene_name")

Author(s)

Steve Sansom

Examples

## Not run: 
ann_hs <- fetchAnnotation(species="hs")
ann_mm <- fetchAnnotation(species="mm")

## End(Not run)

sansomlab/gsfisher documentation built on July 7, 2022, 4:21 a.m.