getFeature {biomaRt}R Documentation

Retrieves Feature starting from a gene symbol and array identifier

Description

This function function retrieves features representing a certain gene given a gene symbol array identifier

Usage

getFeature( symbol, OMIM, OMIMID, GO, GOID, array, chromosome, start, end, type, mart)

Arguments

symbol gene symbol
OMIM OMIM term e.g. diabetes
OMIMID OMIM identifier
GO GO term
GOID GO identifier
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()
chromosome chromosome, can be used without start and end positions
start start on chromosome
end end on chromosome
type type of input identifier, this is either locuslink, embl or refseq.
mart object of class Mart, containing connections to the BioMart databases. You can creat such an object using the function martConnect.

Author(s)

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

Examples

if(interactive()){
mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl")

#example using affy id from Ensembl

feat = getFeature( symbol = "TP53", array = "affy_hg_u95av2", mart = mart)
show(feat)

martDisconnect(mart = mart)
}

[Package biomaRt version 1.8.2 Index]