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
> >>                                     <Rle>  <Rle> <character> <integer>
> >>          [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
> >>              <integer> <integer> <integer> <integer>
> >>          [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 <hpages@fhcrc.org
> >> >> <mailto:hpages@fhcrc.org>>:
> >> >>
> >> >>> 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 <mailto: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 <mailto: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
>
> _____________________________________________________________
>
>

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