getGene: Retrieves gene annotation information given a vector of...

In grimbough/biomaRt: Interface to BioMart databases (i.e. Ensembl)

Retrieves gene annotation information given a vector of identifiers

Description

This function retrieves gene annotations from Ensembl given a vector of identifiers. Annotation includes chromsome name, band, start position, end position, gene description and gene symbol. A wide variety of identifiers is available in Ensembl, these can be found with the listFilters function.

Usage

getGene( id, type, mart)

Arguments

id	vector of gene identifiers one wants to annotate
type	type of identifier, possible values can be obtained by the listFilters function. Examples are entrezgene_id, hgnc_symbol (for hugo gene symbol), 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

Examples

if(interactive()){

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

#example using affy id

g = getGene( id = "1939_at", type = "affy_hg_u95av2", mart = mart)
show(g)

#example using Entrez Gene id

g = getGene( id = "100", type = "entrezgene_id", mart = mart)
show(g)
}

grimbough/biomaRt documentation built on Feb. 11, 2024, 8:20 p.m.