[Bioc-sig-seq] GRanges tabulate the coverage

[Patrick Aboyoun]

Dario,
Thanks for the bug report. This issue is with the 
table,AtomicList-method when the sum(elementLengths(atomicList)) > 
2^31-1. I'll submit a patch to IRanges within the day.

Cheers,
Patrick


On 8/5/10 8:00 PM, Dario Strbenac wrote:
> Hello,
>
> I'm encountering a problem where I can tabulate coverage results when I've got a GRanges object without seqlengths in it, but when I put seqlengths in it, it gives an error about negative length vectors. Here is my small example.
>
> library(GenomicRanges)
> library(BSgenome.Hsapiens.UCSC.hg18)
>
> chrs = paste("chr", c(1:22, "X", "Y"), sep = "")
> myGR<- GRanges(seqnames = c("chr1", "chr3", "chr3", "chr3"), ranges = IRanges(100, width = 200), strand = '+')
> coverage<- colSums(table(coverage(resize(myGR, 300))))
>
> seqlengths(myGR)<- seqlengths(Hsapiens)[chrs]
> coverage<- colSums(table(coverage(resize(myGR, 300))))
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
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