[Bioc-devel] rtracklayer::import( as = 'NumericList' ) doesn't work with more than 1 range

[Leonardo Collado Torres]

Thank you Valerie for the bug fix and Michael for the explanation!

Cheers,
Leo

On Wed, May 20, 2015 at 2:28 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> I guess I would say that the summary stuff is sort of an estimate that is
> useful for e.g. visualization, rather than an exact quantification.
>
> On Wed, May 20, 2015 at 10:56 AM, Valerie Obenchain <vobencha at fredhutch.org>
> wrote:
>
>> Hi Leo,
>>
>> Thanks for reporting the bug with import. The problem was in how the
>> length of the output was computed. This has been fixed in both release
>> (1.28.3) and devel (1.29.6).
>>
>> I'll let Michael answer the summary() question.
>>
>> Valerie
>>
>>
>>
>> On 05/19/2015 12:10 PM, Leonardo Collado Torres wrote:
>>
>>> Hi,
>>>
>>> While playing around with importing BigWig files I found that
>>> import.bw() fails when you use a `which` or `selection` that has more
>>> than one range and you specify `as = 'NumericList'`. The code and
>>> output are available at
>>> https://gist.github.com/lcolladotor/a0eafc335a2738de42f6. From the
>>> BigWigFile-class documentation, I suspect that this is a bug. The same
>>> thing happens even if I use BigWigFileSelection() instead of supplying
>>> a GRanges of length 2.
>>>
>>> Also, what is the summary() function doing when you calculate the
>>> mean? I would expect it to be the same mean if I import the data as an
>>> Rle and calculate the mean there. See (after running the code in the
>>> gist):
>>>
>>>  x <- import(BigWigFile(bw[1]), as = 'RleList')
>>>> mean(x)
>>>>
>>>       chr21
>>> 0.02474045
>>>
>>>> summary(BigWigFile(bw[1]), type = 'mean')[[1]]$score
>>>>
>>> [1] 0.9037462
>>>
>>>> mean(x[x > 0])
>>>>
>>>     chr21
>>> 1.202603
>>>
>>> It's not the mean of the non-zero positions either.
>>>
>>>
>>> Cheers,
>>> Leo
>>>
>>>
>>> Leonardo Collado Torres, PhD Candidate
>>> Department of Biostatistics
>>> Johns Hopkins University
>>> Bloomberg School of Public Health
>>> Website: http://www.biostat.jhsph.edu/~lcollado/
>>> Blog: http://lcolladotor.github.io/
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
>> --
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, Seattle, WA 98109
>>
>> Email: vobencha at fredhutch.org
>> Phone: (206) 667-3158
>>
>>
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>>
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