[BioC] VariantAnnotation updated - error in predictCoding

[Valerie Obenchain]

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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