[BioC] VariantAnnotation updated - error in predictCoding
Valerie Obenchain
vobencha at fhcrc.org
Tue Apr 24 20:00:49 CEST 2012
See ?predictCoding for details.
When a VCF is supplied as the query the varAllele is taken from
alt(VCF). If the query is a GRanges you need to supply the varAllele.
In your example below you create the varAllele but don't use it in the
predictCoding() call.
Valerie
On 04/24/2012 09:13 AM, bnorthoff at web.de wrote:
> Hi there, i am a bit confused concerning the varAllele by using GRanges:
>
> snp1 = GRanges(seqnames="chr2", ranges=IRanges(start=28920, width=1),
> refAllele=DNAStringSet("G"), varAllele=DNAStringSet("A"))
> library(TxDb.Mmusculus.UCSC.mm9.knownGene)
> txdb = TxDb.Mmusculus.UCSC.mm9.knownGene
> coding = predictCoding(query=snp1, subject=txdb, seqSource=Mmusculus)
>
> I thought the varAllele was given by the GRanges, isn't it?
>
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