Hi Xavier,

Thanks so much for the information.  I'll upgrade my R version to R 2.14,
then.

Cheers,

Adriana

On Mon, Nov 14, 2011 at 3:16 AM, Xavier de Pedro <xavier.depedro@vhir.org>wrote:

> 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@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
>>>>>
>>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>>
>>>>>
>

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