[BioC] problems with strand in predictCoding

[Bernd]

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
> 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found

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!