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

[Xavier de Pedro]

As far as I remember, only available since R 2.14.
Cheers
Xavier

On 11/11/11 18:16, Adriana Munoz wrote:
> Hi Valerie,
>
> Thanks for the information.  I used the filter you mentioned and it works.
>   I'd like to try the Variant Annotation package that you mentioned to
> get where my variant is located (coding, non-coding, utr, etc.) , too, but
> I got the following error message in my Mac:
> "Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>    package ‘VariantAnnotation’ is not available (for R version 2.13.2)"
>
> Then, I tried loading the package in Windows that has R version 2.12., but
> I  the following error message:
> "Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>    package ‘VariantAnnotation’ is not available"
>
> May I ask you if you know by chance  what version of R you were running for
> the Variant Annotation package? or do you know of any attributes and
> filters in Biomart to get where my variant is located (coding, non-coding,
> utr, etc.)?
>
> Thanks,
>
> Adriana
>
> On Tue, Nov 8, 2011 at 7:37 PM, Valerie Obenchain<vobencha at fhcrc.org>wrote:
>
>> Hi Adriana,
>>
>> I believe the filter you want is consequence_type. Take a look at the
>> filters available to you with,
>>
>>     listFilters(snpmart)
>>
>> You may also want to take a look at the VariantAnnotation package. There
>> are functions
>>
>>     ?locateVariants
>>     ?predictCoding
>>
>> 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.
>>
>> Valerie
>>
>>
>>
>>
>>
>>
>> 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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>>>>