getGene {biomaRt}R Documentation

Retrieves Gene information

Description

This function function retrieves gene information from Ensemble given a gene identifier

Usage

getGene( id = NULL, type = NULL, array = NULL, species = NULL, db = "ensembl", mart = NULL, output = "martTable" )

Arguments

id gene identifier
type type of identifier, value should be either affy, entrezgene, embl, hugo, ensembl or refseq
array array identifier only to be used if gene identifiers are from affy arrays. An overview of the accepted identifiers can be obtained with the function: getAffyArrays()
species species, only to be used if type equals locuslink. Accepted values for species can be retrieved with the function getSpecies()
db database you want to query either ensembl (default) or vega
mart object of class Mart, containing connections to the BioMart databases. You can creat such an object using the function martConnect.
output desired output type, either object of class martTable or GeneObject

Author(s)

Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck

See Also

Examples

## Not run: 
mart <- martConnect()

#example using affy id from Ensembl

getGene( id = "1939_at", array = "hg_u95av2", mart = mart)

#example using locuslink id from vega

getGene( id = 100, type = "entrezgene", species = "hsapiens", db = "vega", mart = mart)

martDisconnect(mart = mart)
## End(Not run)

[Package biomaRt version 1.0.4 Index]