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

Description Usage Arguments Author(s) Examples

View source: R/biomaRt.R

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

1
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, 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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
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", mart = mart)
show(g)
}

biomaRt documentation built on Nov. 1, 2018, 3:34 a.m.