getGO {biomaRt}R Documentation

Retrieves GO information

Description

This function retrieves GO identifiers, GO descriptions and evidence codes from Ensembl given a vector of gene identifier. A wide variety of gene indentifiers can be used as inputs. The list of possible identifiers that can be used as input, can be found using the listFilters function.

Usage

getGO( id, type, mart)

Arguments

id gene identifier
type type of identifier, possible values can be obtained by the listFilters function. Examples are entrezgene, hgnc_symbol (for hugo gene sy mbol), ensembl_gene_id, unigene, agilentprobe, affy_hg_u133_plus_2, refseq_dna, etc.
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.stat.berkeley.edu/~steffen

Examples

if(interactive()){

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

#example using affy id

go = getGO( id = "1939_at", type = "affy_hg_u95av2", mart = mart)
show(go)

#example using entrezgene id

go = getGO( id = 672, type = "entrezgene", mart = mart)
show(go)
}

[Package biomaRt version 1.16.0 Index]