[BioC] A problem with getting promoter variants with the function locateVariants (from package VariantAnnotation)

[Valerie Obenchain]

Hi Jarno,

Thanks for the bug report. The problem was in the 
PromoterVariants-method which is new for 2.11. AllVariants calls 
PromoterVariants so that too was broken.

Fixes are in VariantAnnotation 1.4.3 in release and 1.5.9 in devel. 
These will be available through biocLite() by noon Tuesday or in svn 
immediately.

Valerie



On 11/04/2012 05:14 AM, Jarno Tuimala wrote:
> Hello!
>
> I have a script that worked with Bioconductor version 2.10 packages,
> but does not work anymore with the latest 2.11 release. More
> specifically, I've used locateVariants() from package
> VariantAnnotation to locate all variants in a specific vcf file.
>
> With the latest package version I can't get locateVariants() to work
> with values AllVariants() or PromoterVariants() for the region
> argument (see below for an example). This seems to work with the
> example file structural.vcf from the same package, though.
>
> What am I doing wrong?
>
> Of course, as a quick fix I can generate coding, intronic etc.
> variants as separate objects, and then combine them together, but it
> would be simpler to get them all with a single function call.
>
> - Jarno
>
>
>> input.vcf<-system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
>> library(VariantAnnotation)
>> genome<-"hg19"
>> vcf<-readVcf(input.vcf, genome)
>> rd<- rowData(vcf)
>> newnames<- paste("chr", seqlevels(vcf), sep="")
>> names(newnames)<- seqlevels(vcf)
>> vcf_adj<- renameSeqlevels(vcf, newnames)
>> rd_adj<- renameSeqlevels(rd, newnames)
>> library("TxDb.Hsapiens.UCSC.hg19.knownGene")
>> txdb<- TxDb.Hsapiens.UCSC.hg19.knownGene
>> loc_coding<- locateVariants(vcf_adj, txdb, AllVariants())
> Error in if ((nrx == 0) || (nrx%%lv != 0)) stop(paste(lv, "elements in
> value to replace",  :missing value where TRUE/FALSE needed
>> loc_coding<- locateVariants(vcf_adj, txdb, CodingVariants())
>> loc_coding<- locateVariants(vcf_adj, txdb, PromoterVariants())
> Error in if ((nrx == 0) || (nrx%%lv != 0)) stop(paste(lv, "elements in
> value to replace",  :missing value where TRUE/FALSE needed
>> sessionInfo()
> R version 2.15.2 Patched (2012-11-01 r61067)
> Platform: i386-w64-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=Finnish_Finland.1252  LC_CTYPE=Finnish_Finland.1252
> LC_MONETARY=Finnish_Finland.1252 LC_NUMERIC=C
> LC_TIME=Finnish_Finland.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] VariantAnnotation_1.4.2                 Rsamtools_1.10.1
>                Biostrings_2.26.2
> TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 GenomicFeatures_1.10.0
>   [6] AnnotationDbi_1.20.2                    Biobase_2.18.0
>                GenomicRanges_1.10.3                    IRanges_1.16.4
>                         BiocGenerics_0.4.0
> [11] BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
>   [1] biomaRt_2.14.0     bitops_1.0-4.1     BSgenome_1.26.1
> DBI_0.2-5          parallel_2.15.2    RCurl_1.95-1.1
> RSQLite_0.11.2     rtracklayer_1.18.0 stats4_2.15.2      tools_2.15.2
>       XML_3.95-0.1       zlibbioc_1.4.0
>
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