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, species, 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()
species species, only to be used if type equals locuslink. Accepted values for species can be retrieved by the function getSpecies()
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

See Also

Examples

if(interactive()){
mart <- martConnect()

#example using affy id

interpro = getINTERPRO( id = "1939_at", array = "hgu95av2", mart = mart)
show(interpro)

#example using locuslink id

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

martDisconnect(mart = mart)
}

[Package biomaRt version 1.4.0 Index]