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

[Valerie Obenchain]

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/
>
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>


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