[BioC] Welcome to the "Bioconductor" mailing list

[Hervé Pagès]

Hi Adriana,

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On 11-11-02 07:17 AM, Adriana Munoz wrote:
> Hello,
>
> I'd like to ask you if there is an attribute for SNP function class for
> variation datasets in biomaRt that is equivalent to the field
> 'function-class' (or fxn-class field) in the dbSNP database (NCBI) and
> a related filter.  I think biomaRt is great and I'd
> really like to use biomaRt to extract information on SNP function class
> such as synonymous-codon, nonsynonymous, non-genic.

Which mart/dataset are you looking at? Did you try listAttributes()?

Maybe an alternative to using biomaRt would be for you to have a look
at the VariantAnnotation package (new in BioC 2.9).

Cheers,
H.

>
> Any help will be appreciated.
>
> Thanks,
>
> Adriana
>
>
> On Wed, Nov 2, 2011 at 10:10 AM,<bioconductor-request at r-project.org>  wrote:
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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