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.mich...@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 <voben...@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@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: voben...@fredhutch.org >> Phone: (206) 667-3158 >> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel