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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