[BioC] Error in locateVariants

[Valerie Obenchain]

Hi Jolly,

I need a reproducible example in order to help. Are 'rd' and 
'myGRangesList' too large to send? Also provide the output of sessionInfo().

Valerie


On 07/24/2013 11:38 AM, Jolly Shrivastava wrote:
> Hello Valerie,
>
> I am running VariantAnnotation package to locate the position of SNPs using
> locateVariants.
>
> The commands that I gave to extract vcf file and the gff file are as
> follows:
>
> ###Reading the vcf file
> vcf1<-readVcf("CGTACG_filteredSNPS.vcf","Pinfestans.fa")
> rd<-rowData(vcf1)
>
> ####imported and converted the gff3 file to GRangesList object
> subject<-import.gff("annotation.gff3")
> myGRanges<-as(subject,"GRanges")
> myGRangesList<-GRangesList(myGRanges)
>
>
> ### made sure that both of them have same sequence levels
> rd<-keepSeqlevels(rd,intersect(seqlevels(rd),seqlevels(myGRangesList))
> myGRangesList<-keepSeqlevels(myGRangesList,intersect(seqlevels(rd),seqlevels(myGRangesList))
>
> ###Ran the locateVariants command
> variants_found<-locateVariants(rd,myGRangesList,CodingVariants())
>
> ###Got the following error
> Error in DataFrame(...) : different row counts implied by arguments
>
> Can you please point to what I am doing wrong?
>
> Regards
> Jolly
>
>