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