Dario,
I just checked in a fix to IRanges in BioC 2.6 (IRanges 1.6.13) and BioC
2.7 (IRanges 1.7.17) that fixes the issue with the table method for
AtomicList objects. Previous there was just a table,AtomicList-method,
which was written with CompressedAtomicList objects in mind. I have
moved the old method definition over to a
table,CompressedAtomicList-method and have created a new
table,SimpleAtomicList-method. For your use case, this new method will
be much faster since it avoids unlisting the data and replicating the
element names. These changes will become available from bioconductor.org
within 36 hours.
> suppressMessages(library(GenomicRanges))
> library(BSgenome.Hsapiens.UCSC.hg18)
Loading required package: BSgenome
Loading required package: Biostrings
> chrs <- paste("chr", c(1:22, "X", "Y"), sep = "")
> myGR <- GRanges(seqnames = c("chr1", "chr3", "chr3", "chr3"), ranges
= IRanges(100, width = 200), strand = '+')
> colSums(table(coverage(resize(myGR, 300))))
0 1 3
198 300 300
> seqlengths(myGR) <- seqlengths(Hsapiens)[chrs]
> colSums(table(coverage(resize(myGR, 300))))
0 1 3
3080418880 300 300
> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-08-01 r52659)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg18_1.3.16 BSgenome_1.17.6
[3] Biostrings_2.17.27 GenomicRanges_1.1.20
[5] IRanges_1.7.17
loaded via a namespace (and not attached):
[1] Biobase_2.9.0
Cheers,
Patrick
On 8/5/10 11:55 PM, Patrick Aboyoun wrote:
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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