[BioC] BiomaRt - Flanking regions

[Ovokeraye Achinike-Oduaran]

Thanks Jim.

I will try out the ?getSequence command and see what options I get.
What I am actually trying to do is to retreive possible regulatory
SNPs 1Kb upstream of the genes on my list.

Thanks again. I'll see what that gives me.

Kind regards,

Avoks

On 7/16/12, James W. MacDonald <jmacdon at uw.edu> wrote:
> Hi Avoks,
>
> It depends on what you mean by 'flanking gene regions'. Do you want the
> sequences? The coordinates?
>
> Assuming you want the sequences:
>
> library(biomaRt)
> ?getSequence
>
> Best,
>
> Jim
>
>
>
> On 7/16/2012 9:53 AM, Ovokeraye Achinike-Oduaran wrote:
>> Hi all,
>>
>> I had a quick question on how to get flanking gene regions using
>> biomaRt to access Biomart. I used listAttributes() to see what my
>> options were but I could not quite figure it out. Any ideas?
>>
>> Thanks and kind regards.
>>
>> -Avoks
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>