getFeature {biomaRt}R Documentation

Retrieves identifiers starting from a gene symbol, chromosomal position or GO identifier

Description

This function function retrieves identifiers representing a certain gene given a gene symbol, chromosomal positions or GO identifier

Usage

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

Arguments

symbol gene symbol
OMIMID OMIM identifier
GOID GO identifier
chromosome chromosome, can be used without start and end positions
start start on chromosome
end end on chromosome
type type of identifier that needs to be retrieved, possible values can be obtained by the listFilters function. Examples are entrezgene, hgnc_symbol (for hugo gene symbol), ensembl_gene_id, unigene, agilentprobe, refseq_dna, affy_hg_u133_plus_2, etc.
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

Examples

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

#example using affy id from Ensembl

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

[Package biomaRt version 1.10.1 Index]