[BioC] problems with strand in predictCoding

[Valerie Obenchain]

On 04/25/2012 12:28 AM, Bernd wrote:
> Hi there,
>
> Jeremiah Degenhardt<degenhardt.jeremiah at ...>  writes:
>
>> Hello BioC,
>>
>> I am using the predictCoding function in the VariantAnnotation package
>> and have run into a few issues.
>>
>> The first issue that I found is a small one. While I can supply any
>> txdb object that I want to the predictCoding, the function seems to
>> still be looking for TxDb.Hsapiens.UCSC.hg19.knownGene. Running
>> predict coding without this package installed results in the following
>> error:
>>
>> Error in isCircular(TxDb.Hsapiens.UCSC.hg19.knownGene) :
>>    error in evaluating the argument 'x' in selecting a method for
>> function 'isCircular': Error: object
>> ''
> Since I am using the library TxDb.Mmusculus.UCSC.mm9.knownGene this is a problem
> for my analysis of snps in mice. I get the same error by using this code:
>
> library(BSgenome.Mmusculus.UCSC.mm9)
> library(TxDb.Mmusculus.UCSC.mm9.knownGene)
>
> txdb = TxDb.Mmusculus.UCSC.mm9.knownGene
>
> snp1 = GRanges(seqnames="chr2", ranges=IRanges(start=28920573, width=1),
> strand="+", varAllele=DNAStringSet("A"))
>
> predictCoding(query=snp1, subject=txdb, seqSource=Mmusculus,
> varAllele=values(snp1)$varAllele)
>
> Is there any solution?
> Tanks a lot!
>

The txdb error has been fixed in VariantAnnotation 1.2.6 in release and 
1.3.8 in devel. I'm currently working on the predictCoding strand issue 
and will post back here when it's fixed.

Valerie
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