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

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>:

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 , philip.lijnzaad at gmail.com
P.O. Box 85060, 3508 AB Utrecht
(Universiteitsweg 100, 3584 CG Utrecht)
The Netherlands
tel: +31 (0)8875 68464


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