[BioC] Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?

Valerie Obenchain vobencha at fhcrc.org
Wed Nov 9 01:37:02 CET 2011

Hi Adriana,

I believe the filter you want is consequence_type. Take a look at the 
filters available to you with,


You may also want to take a look at the VariantAnnotation package. There 
are functions


that can tell you where your variant is located (coding, non-coding, 
utr, etc.) and provide the amino acid coding change is for the 
non-synonymous variants. Recently SIFT and PolyPhen scores have been 
made available through db packages
SIFT.Hsapiens.dbSNP132 and PolyPhen.Hsapiens.dbSNP131.


On 11/02/2011 07:33 AM, Adriana Munoz wrote:
>> Hello,
>> I'd like to ask you if there is an attribute to extract SNP function information from variation datasets in biomaRt such as synonymous, nonsynonymous, etc and
>> a related filter.
>> I'm using the following rcode:
> snpmart = useMart("snp", dataset="hsapiens_snp")
>> Any help will be appreciated.
>> Thanks,
>> Adriana
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