getINTERPRO {biomaRt}R Documentation

Retrieves INTERPRO protein domain information

Description

This function retrieves INTERPRO protein domain information using Ensembl and UNIPROT (http://www.ebi.ac.uk/uniprot) given a gene identifier

Usage

getINTERPRO( id, type, array, mart)

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()
mart object of class Mart, containing connections to the BioMart databases. You can create such an object using the function useMart.

Author(s)

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

Examples

if(interactive()){

mart = useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")

#example using affy id

interpro = getINTERPRO( id = "1939_at", array = "affy_hg_u95av2", mart = mart)
show(interpro)

#example using locuslink id

interpro = getINTERPRO( id = 672, type = "entrezgene", mart = mart)
show(interpro)

}

[Package biomaRt version 1.8.2 Index]