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

[Hervé Pagès]

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>:
>
>> 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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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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