[BioC] symbol to location

[Rafael A Irizarry]

perfect. thanks -r


On Tue, 26 Dec 2006, Steffen Durinck wrote:

> 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
> URL: http://home.ccr.cancer.gov/oncology/oncogenomics/
>
> Phone: 301-402-8103
> Address:
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>