Hi Patrick, Since the upgrade yesterday morning, this problem seems to have gone away. That is good news, I guess.
I'll report to the list if I bump into it again. Thank you very much for trying to solve the problem. Ivan Ivan Gregoretti, PhD National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health On Mon, Apr 26, 2010 at 4:42 PM, Patrick Aboyoun <[email protected]> wrote: > Ivan, > I can't reproduce this. Could you provide an example? > > Thanks, > Patrick > > > On 4/23/10 2:28 PM, Ivan Gregoretti wrote: >> >> Hi all, >> >> coverage(), naughty boy! >> >> I have two GRanges instances >> >> # my 100 million tags >> >>> >>> class(B) >>> >> >> [1] "GRanges" >> attr(,"package") >> [1] "GenomicRanges" >> >> # a few ChIP-seq peaks >> >>> >>> class(P) >>> >> >> [1] "GRanges" >> attr(,"package") >> [1] "GenomicRanges" >> >> # Now I want to keep only the tags in-peak >> >>> >>> BP<- B[B %in% P,] >>> >> >> # Are you ok BP? >> >>> >>> class(BP) >>> >> >> [1] "GRanges" >> attr(,"package") >> [1] "GenomicRanges" >> # Good. >> >> # Now, whilst coverage(B) and coverage(P) work, BP crashes >> >>> >>> coverage(BP) >>> >> >> Error in coverage.normargWidth(width, length(x)) : >> 'x' has no element and 'width' is NULL >> >> >> BP is, I understand, I subset of B. Why would it crash coverage()? >> >> >> Thank you, >> >> Ivan >> >> >>> >>> sessionInfo() >>> >> >> R version 2.12.0 Under development (unstable) (2010-03-25 r51410) >> x86_64-unknown-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> LC_TIME=en_US.UTF-8 >> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=C >> LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> LC_ADDRESS=C >> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 >> LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BSgenome.Mmusculus.UCSC.mm9_1.3.16 chipseq_0.3.5 >> [3] ShortRead_1.5.21 lattice_0.18-3 >> [5] BSgenome_1.15.19 Biostrings_2.15.25 >> [7] GenomicRanges_0.0.9 IRanges_1.5.70 >> [9] rtracklayer_1.7.11 RCurl_1.3-1 >> [11] bitops_1.0-4.1 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.6.1 grid_2.12.0 hwriter_1.1 tools_2.12.0 XML_2.6-0 >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
