Dear James,

Thank you. This works brilliantly. However it now returns ENSG ids
(previously entrez IDs).

When I try to map these into gene symbols using og.Hs.egENSEMBL, about 20%
of ENSG ids are not found. Should I use another database/package to do this
conversion?


On Fri, Oct 18, 2013 at 2:27 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Adai,
>
> See makeTranscriptDbFromBiomart() in the GenomicFeatures package.
>
> Best,
>
> Jim
>
>
>
>
> On Friday, October 18, 2013 9:18:46 AM, Adaikalavan Ramasamy wrote:
>
>> Hi there,
>>
>> I am using the R package TxDb.Hsapiens.UCSC.hg19.**knownGene to annotate
>> SNPs
>> using the locateVariants() function from the VariantAnnotation package.
>>
>> For reasons of compatibility with other pipelines I developed, I would
>> like
>> to use Ensembl/Gencode annotation. Is there a package for this? Otherwise
>> please advice on how best to generate this myself.
>>
>> Thank you.
>>
>> Regards, Adai
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
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>

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