[BioC] VariantAnnotation updated - error in predictCoding

[Valerie Obenchain]

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?
>>
>>
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