Hey Patrick, Just pulled this from SVN, thanks! -steve On Mon, Apr 12, 2010 at 4:10 PM, Patrick Aboyoun <paboyoun at="" fhcrc.org=""> wrote: > Steve, > I'm not sure if this is a doc bug or a bug in code, but either way it was a > bug. Given that it would be reasonable to recycle the bounds argument to be > equilength with x, I patched IRanges in BioC 2.6 to perform the recycling. > This new version of the IRanges package will be available from > bioconductor.org within 36 hours. > >> reflect(IRanges(c(1,20,30), width=5), IRanges(1, 34)) > IRanges of length 3 > ? ?start end width > [1] ? ?30 ?34 ? ? 5 > [2] ? ?11 ?15 ? ? 5 > [3] ? ? 1 ? 5 ? ? 5 >> >> sessionInfo() > R version 2.11.0 beta (2010-04-12 r51689) > i386-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] IRanges_1.5.76 > > > > Cheers, > Patrick > > On 4/12/10 12:22 PM, Steve Lianoglou wrote: >> >> Hi all, >> >> I was messing around with the IRanges::reflect method, wanting to >> reflect an IRanges object (with many inner ranges) within 1 large >> bounds. For instance, something like so: >> >> R> ?reflect(IRanges(c(1,20,30), width=5), IRanges(1, 34)) >> >> However I get this message: >> >> Error in reflect(IRanges(c(1, 20, 30), width = 5), IRanges(1, 34)) : >> ? 'bounds' must be a Ranges object of length equal to that of 'x' >> >> Which, I guess, is fine, because I can always do: >> >> R> ?reflect(IRanges(c(1,20,30), width=5), IRanges(c(1,1,1), c(34,34,34))) >> >> But the section that address "reflect" in ?reflect says: >> >> ? ? reflect "reflects" or reverses each range in x relative to the >> ? ? corresponding range in bounds, which is *recycled as necessary*. >> >> (ASCII-emphasis mine) >> >> But it seems that neither the `bounds` or `x` var is recycled anyway I >> slice it. So, I'm curious if there's a discrepancy between the >> documentation and (i) the implementation; or (ii) my understanding. >> >> btw - I'm using IRanges_1.5.74 >> >> Thanks, >> -steve >> >> > > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact