In theory we should be able to back-port this change. I have no idea why it is not making it into the release. It was committed after the circular stuff (which breaks serialized object compatibility), but does not depend on it.
Michael On Fri, Oct 1, 2010 at 9:00 AM, Steve Lianoglou < [email protected]> wrote: > Hi, > > On 09/14/2010 01:46 PM, Michael Lawrence wrote: > > I just checked in some changes to IRanges, that make this method work: > > > > setMethod("resize", "GenomicRanges", > > function(x, width, fix = "start", use.names = TRUE) > > { > > revFix <- c(start = "end", end = "start", center = "center") > > fix <- ifelse(strand(x) == "-", revFix[fix], fix) > > ranges <- > > resize(ranges(x), width = width, fix = fix, use.names = > > use.names) > > if (!IRanges:::anyMissing(seqlengths(x))) { > > start(x) <- start(ranges) > > end(x) <- end(ranges) > > } else { > > x <- clone(x, ranges = ranges) > > } > > x > > } > > ) > > > > That will accept the fix argument, ... > > Sorry to bring up an old thread -- but I want to use the "fix" > parameter in resizing GRanges objects in some of my code. > > I see that this change has been made to SVN, but if I'm not mistaken, > it seems to not be coming to the GRanges stuff that's scheduled to > land w/ BioC 2.7/R-2.12? > > Is this intentional? If so, how come? I don't think it'll break > backwards compatibility, right? > > Maybe an oversight? (perhaps on my part, or "yours" :-)? > > For now I think I'm just going to take this code and override the > BioC-2.7 version of resize, since I'd like to use it but can't upgrad > to svn GRanges since some of my stuff is getting hosed with the > "circular" stuff that's starting to be introduced. > > 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<http://cbio.mskcc.org/%7Elianos/contact> > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
