[BioC] symbol to location

[Steffen Durinck]

Hi Rafa,

You can do this easily with biomaRt, here's the code:

library(biomaRt)
ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl")
symbols = c("AATK","ABCB1")
getBM(c("hgnc_symbol","chromosome_name","start_position","end_position","band","strand"), 
filters="hgnc_symbol", values=symbols,mart=ensembl)

it gives:

 >   hgnc_symbol chromosome_name start_position end_position   band strand
1        AATK              17       76705703     76754467  q25.3     -1
2        AATK              17       76705703     76754467  q25.3     -1
3       ABCB1               7       86970884     87180500 q21.12     -1

Note that AATK is twice in the output because it has 2 transcripts in 
Ensembl.

best,
Steffen

Rafael A Irizarry wrote:
> Hi!
>
> Can you recommend your favorite way to go from 
> gene symbols, such as AATK, ABCB1, 
> etc.. to genomic location?
>
> what ive come up with seems way to cumbersome.
>
> -r
>
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-- 
Steffen Durinck, Ph.D.

Oncogenomics Section
Pediatric Oncology Branch
National Cancer Institute, National Institutes of Health
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