getGene {biomaRt} | R Documentation |
This function function retrieves gene information from Ensemble given a gene identifier
getGene( id = NULL, type = NULL, array = NULL, species = NULL, db = "ensembl", mart = NULL, output = "martTable" )
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 |
Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck
## 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)