getGene {biomaRt} | R Documentation |
This function function retrieves gene information from Ensemble given a gene identifier
getGene( id, type, array, species, db = "ensembl", mart)
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. |
Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck
if(interactive()){ mart <- martConnect( biomarts = c("ensembl","vega")) #example using affy id from Ensembl g = getGene( id = "1939_at", array = "hg_u95av2", mart = mart) show(g) #example using locuslink id from vega g = getGene( id = 100, type = "entrezgene", species = "hsapiens", db = "vega", mart = mart) show(g) martDisconnect(mart = mart) }