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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