[BioC] DNAStringSet_translate error in predictCoding()
Valerie Obenchain
vobencha at fhcrc.org
Thu Nov 1 05:08:06 CET 2012
Hi Rebecca,
It looks like your ALT variable may contain structural variants. When
structural variants are present in a vcf file, readVcf() will convert
this to a CharacterList instead of a DNAStringSetList. Try,
alt(vcf)
and see if you have a DNAStringSetList. If instead you have a
CharacterList, see this thread for how you can subset the vcf on
non-structural variants.
https://stat.ethz.ch/pipermail/bioconductor/2012-October/048370.html
Valerie
On 10/31/12 16:44, sun wrote:
> Hi all,
>
> I got an error when I used predictCoding() in VariantAnnotation package.
>
>> coding<- predictCoding(vcf, txdb, injected_Arabi)
> Error in .Call2("DNAStringSet_translate", x, DNA_BASE_CODES, lkup,
> skipcode, :
> in 'x[[24606]]': not a base at pos 3
>
> How can I get the value of x[[24606]]? Any suggestion for the debugging?
>
> Thanks,
>
> Rebecca
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> 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
More information about the Bioconductor
mailing list