On a second look I see you did not create the varAllele separately as I thought you did. You've probably used an earlier version of predictCoding where the varAllele was taken from the elementMetadata in the GRanges object. That approach was fragile so the varAllele is now taken from the VCF object or a GRanges with varAllele specified as a DNAStringSet. The current versions of VariantAnnotation in both release and devel take this new approach. Valerie On 04/24/2012 11:00 AM, Valerie Obenchain wrote: > 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? >> >> >> Ihr WEB.DE Postfach immer dabei: die kostenlose WEB.DE Mail App >> f?r iPhone >> und Android. >> [1]https://produkte.web.de/freemail_mobile_ startseite/ >> >> References >> >> 1. https://produkte.web.de/freemail_mobile_startseite/ >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor