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

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", mart = mart)
show(g)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(biomaRt)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/biomaRt/getGene.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getGene
> ### Title: Retrieves gene annotation information given a vector of
> ###   identifiers
> ### Aliases: getGene
> ### Keywords: methods
> 
> ### ** 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)
Error in martCheck(mart, "ensembl") : 
  This function only works when used with the ensembl BioMart.
Calls: getGene -> martCheck
Execution halted