[Bioc-devel] coverage(gr, weight='score') does not work when score(gr) is an Rle

On 04/17/2015 10:00 AM, Michael Lawrence wrote:

Is that the case here? He has an Rle as an mcol in the GRanges, so in
general expanding it will not align with the other components.

Not sure what you mean. Can you give an example?

H.

On Fri, Apr 17, 2015 at 9:42 AM, Herv? Pag?s <hpages at fredhutch.org
<mailto:hpages at fredhutch.org>> wrote:

    Hi,

    I think we should just expand the Rle internally. That will produce
    a numeric vector of the length of the GRanges i.e. it will be the
    same size as the start and end components of the GRanges object
itself.
    No big deal at all.

    I'll make that change.

    H.


    On 04/17/2015 09:00 AM, Michael Lawrence wrote:

        Ideally it should be supported, but it would take some work as
        the coverage
        stuff is all in C. Could you give more details on your use case?
For
        example, if you already have a range for every position on the
        chromosome,
        you could just extract the score column. I'm guessing it's more
        complicated
        than that. If the zeros are the problem, you could just subset
        the GRanges
        to remove the ranges with zero score, and then coerce the score
        to numeric
        before calling coverage.

        Michael

        2015-04-17 8:00 GMT-07:00 Philip Lijnzaad
        <p.lijnzaad at umcutrecht.nl <mailto:p.lijnzaad at umcutrecht.nl>>:


            Dear all,  I'm puzzled by the following behaviour:

            Given

                  n <- 10
                  gr <- GRanges(seqnames=Rle('A', n),
                                ranges=IRanges(1:n, width=1),
                                score=Rle(5,n))
            If I do

                  coverage(gr,weight='score')

            I get

                  Error in .normarg_shift_or_weight(weight, "weight", x) :
                    'weight' must be a numeric vector, a single string,
            or a list-like
            object

            Surely 'score' should be allowed to be an Rle? Especially
            given the
            fact that the return value of coverage(x,weight="score")
            when score is
            plain numeric vector is always an Rle ! Is this the expected
            behaviour?
            If so, I would argue that violates the principle of least
            suprise :-)

            The background to this is that I do numerical analysis on
            derived
            numerical data along my chromosomes. It contains many
            contiguous zeroes so it would be wasteful to cast
            everything down using as.numeric().

            This is R version 3.01 on x86_64 Linux, Bioconductor version
            2.13,

                package.version("IRanges")

            [1] "1.20.7"

                package.version("GenomicRanges")

            [1] "1.14.4"

            Regards,


            Philip


            --
            Philip Lijnzaad, PhD
            Molecular Cancer Research
            University Medical Center (UMC), Utrecht
            Stratenum room 2.211
            IM: plijnzaad at jabber.org <mailto:plijnzaad at jabber.org> ,
            philip.lijnzaad at gmail.com <mailto:philip.lijnzaad at gmail.com>
            P.O. Box 85060, 3508 AB Utrecht
            (Universiteitsweg 100, 3584 CG Utrecht)
            The Netherlands
            tel: +31 (0)8875 68464 <tel:%2B31%20%280%298875%2068464>



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Herv? Pag?s

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