Looks like there's a problem preventing newer GenomicRanges from being published. Doesn't look like it's my fault this time ;) Only option is to grab from svn right now. Michael On Mon, Oct 28, 2013 at 7:00 AM, Stefanie Tauber < stefanie.tauber@univie.ac.at> wrote: > Here is my SessionInfo, > GenomicRanges as well as IRanges should be up-to-date. > > R Under development (unstable) (2013-10-15 r64056) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Rsamtools_1.15.2 Biostrings_2.31.0 GenomicFeatures_1.15.2 > [4] AnnotationDbi_1.25.2 Biobase_2.23.1 GenomicRanges_1.15.1 > [7] XVector_0.3.0 IRanges_1.21.5 BiocGenerics_0.9.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.19.0 bitops_1.0-6 BSgenome_1.31.0 DBI_0.2-7 > [5] RCurl_1.95-4.1 RSQLite_0.11.4 rtracklayer_1.23.1 stats4_3.1.0 > [9] tools_3.1.0 XML_3.98-1.1 zlibbioc_1.9.0 > > > Best, > Stefanie > > On Mo, 28.10.2013, 14:56, Michael Lawrence wrote: > > Probably need to update GenomicRanges. > > > > > > On Mon, Oct 28, 2013 at 5:11 AM, Stefanie Tauber < > > stefanie.tauber@univie.ac.at> wrote: > > > >> Hi Hervé, > >> > >> I just wanted to try the new coverage function: > >> > >> # I read in a bam file, human data mapped against the transcriptome > >> x = readGAlignments(human_trans_bam) > >> > >> # This is my GAligments object > >> > x > >> GAlignments with 46765032 alignments and 0 metadata columns: > >> seqnames strand cigar qwidth > >> > >> [1] hg19_ensGene_ENST00000237247 + 75M 75 > >> [2] hg19_ensGene_ENST00000371036 - 75M 75 > >> [3] hg19_ensGene_ENST00000371037 - 75M 75 > >> [4] hg19_ensGene_ENST00000471889 - 75M 75 > >> [5] hg19_ensGene_ENST00000377479 + 75M 75 > >> ... ... ... ... ... > >> [46765028] hg19_ensGene_ENST00000344867 - 75M 75 > >> [46765029] hg19_ensGene_ENST00000400848 - 75M 75 > >> [46765030] hg19_ensGene_ENST00000400848 - 75M 75 > >> [46765031] hg19_ensGene_ENST00000400848 - 75M 75 > >> [46765032] hg19_ensGene_ENST00000400829 - 75M 75 > >> start end width ngap > >> > >> [1] 1783 1857 75 0 > >> [2] 690 764 75 0 > >> [3] 1632 1706 75 0 > >> [4] 2121 2195 75 0 > >> [5] 391 465 75 0 > >> ... ... ... ... ... > >> [46765028] 280 354 75 0 > >> [46765029] 509 583 75 0 > >> [46765030] 509 583 75 0 > >> [46765031] 509 583 75 0 > >> [46765032] 179 253 75 0 > >> --- > >> seqlengths: > >> hg19_ensGene_ENST00000237247 ... hg19_ensGene_ENST00000400829 > >> 2580 ... 999 > >> > >> When I want to compute the coverage, I get the following: > >> > cov_x = coverage(x) > >> > >> Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : > >> object '.Ranges.coverage' not found > >> > >> Do you know what I am doing wrong? > >> > >> Thanks, > >> Stefanie > >> > >> > >> > >> On Fr, 25.10.2013, 11:44, Hervé Pagès wrote: > >> > Hi Stephanie, > >> > > >> > Just to let you know that in GenomicRanges 1.14.2, coverage() should > >> > now be much faster on objects with many seqlevels. Should be about > >> > 1000x faster or more if you have 50 000 seqlevels. > >> > > >> > The only case where it's still slow is if many seqlevels are marked as > >> > circular (and have a non-NA seqlength) in seqinfo(x), because for > >> > these seqlevels the coverage vector is still post processed by a > >> > loop in R. Could be a problem if for example people have BAM files > >> > with reads aligned to thousands of bacterial genomes. > >> > > >> > GenomicRanges 1.14.2 and IRanges 1.20.1 should become available thru > >> > biocLite() in the next 24 hours or so. The man pages for the > >> "coverage" > >> > methods have been improved, especially in IRanges. > >> > > >> > Cheers, > >> > H. > >> > > >> > > >> > On 10/18/2013 12:19 AM, Stefanie Tauber wrote: > >> >> Thanks for the answer! > >> >> Just wanted to make sure that I don't miss a relevant feature…. > >> >> > >> >> Best, > >> >> Stefanie > >> >> > >> >> Am 17.10.2013 um 22:07 schrieb Hervé Pagès >> >> >: > >> >> > >> >>> Hi Stephanie, > >> >>> > >> >>> On 10/17/2013 07:37 AM, Stefanie Tauber wrote: > >> >>>> What is the best way to compute the coverage on a ReadGAlignments > >> >>>> object > >> >>>> when I have many, many (about 50 000) seqlevels? > >> >>>> > >> >>>> Just computing coverage(object) is terribly slow due to the huge > >> >>>> amount of seqlevels. > >> >>>> > >> >>>> At the moment, I am subsetting the ReadGAlignments object for each > >> >>>> seqlevel, > >> >>>> I omit the redundant seqlevels and calculate the coverage. > >> >>>> This is fast if you do it for a few seqlevels. > >> >>>> But if one really would like to compute the coverage for each > >> >>>> seqlevel individually, > >> >>>> this really takes a long time.. > >> >>> > >> >>> Yes this is a known weakness in the current implementation of > >> >>> coverage(). It loops over the seqlevels and this loop is currently > >> >>> performed in R, which is slow. Unfortunately this is not the first > >> >>> time someone complains about this. > >> >>> > >> >>> Time for us to bite the bullet I guess. I've just started to work > >> >>> on moving the loop to the C-level. That should speed up things > >> >>> significantly. I'll let you know when this is ready. > >> >>> > >> >>> Thanks for the feedback. > >> >>> H. > >> >>> > >> >>>> > >> >>>> > >> >>>> I would appreciate any comments! > >> >>>> > >> >>>> Best, > >> >>>> Stefanie > >> >>>> > >> >>>> _______________________________________________ > >> >>>> Bioconductor mailing list > >> >>>> Bioconductor@r-project.org > >> >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >>>> Search the archives: > >> >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> >>>> > >> >>> > >> >>> -- > >> >>> Hervé Pagès > >> >>> > >> >>> Program in Computational Biology > >> >>> Division of Public Health Sciences > >> >>> Fred Hutchinson Cancer Research Center > >> >>> 1100 Fairview Ave. N, M1-B514 > >> >>> P.O. Box 19024 > >> >>> Seattle, WA 98109-1024 > >> >>> > >> >>> E-mail: hpages@fhcrc.org > >> >>> Phone: (206) 667-5791 > >> >>> Fax: (206) 667-1319 > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > -- > _____________________________________________________________ > > Stefanie Tauber, PhD > > Center for Integrative Bioinformatics Vienna (CIBIV) > Max F. Perutz Laboratories (MFPL) > Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2 > Dr. Bohr Gasse 9 > A-1030 Wien, Austria > Phone: ++43 +1 / 42772-4030 > Fax: ++43 +1 / 42772-4098 > email: stefanie.tauber@univie.ac.at > > _____________________________________________________________ > > [[alternative HTML version deleted]]