[BioC] Ensembl or Gencode version of TxDb.Hsapiens.UCSC.hg19.knownGene

[James W. MacDonald]

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
>
> 	[[alternative HTML version deleted]]
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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