genoset has an is.unsorted for GenomicRanges. I profiled a bit and found a pretty quick way to do it. My version ignores strand, so it is only proper in some cases. But, maybe it's a head start on a fully general function.
Pete ____________________ Peter M. Haverty, Ph.D. Genentech, Inc. phave...@gene.com On Mon, Nov 2, 2015 at 5:35 PM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > The notion of sortedness is already formally defined, which is why we have > an order method, etc. > > The base is.unsorted implementation for "objects" ends up calling > base::.gt() for each adjacent pair of elements, which is likely too slow to > be practical, so we probably should add a custom method. > > This does bring up the tangential question of whether GenomicRanges should > have an anyNA method that returns FALSE (and similarly an is.na() method), > although we have never defined the concept of a "missing range". > > Michael > > On Mon, Nov 2, 2015 at 4:55 PM, Gabe Becker <becker.g...@gene.com> wrote: > > > Pete, > > > > What does sorted mean for granges? If the starts are sorted but the ends > > aren't does that count? What if only the ends are but the ranges are on > the > > negative strand? > > > > Do we consider seqlevels to be ordinal in the order the levels are > returned > > from seqlevels ()? That usually makes sense, but does it always? > > > > In essence I'm asking if sortedness is a well enough defined term for an > > is.sorted method to make sense. > > > > Best, > > ~G > > On Nov 2, 2015 4:27 PM, "Peter Hickey" <peter.hic...@gmail.com> wrote: > > > > > Hi all, > > > > > > I sometimes want to test whether a GRanges object (or some object with > > > a GRanges slot, e.g., a SummarizedExperiment object) is (un)sorted. > > > There is no is.unsorted,GRanges-method or, rather, it defers to > > > is.unsorted,ANY-method. I'm unsure that deferring to the > > > is.unsorted,ANY-method is what is really desired when a user calls > > > is.unsorted on a GRanges object, and it will certainly return a > > > (possibly unrelated) warning - "In is.na(x) : is.na() applied to > > > non-(list or vector) of type 'S4'". > > > > > > > > > For this reason, I tend to use is.unsorted(order(x)) when x is a > > > GRanges object. This workaround is also used, for example, by minfi > > > ( > https://github.com/kasperdanielhansen/minfi/blob/master/R/blocks.R#L121 > > ). > > > However, this is slow because it essentially sorts the object to test > > > whether it is already sorted. > > > > > > > > > So, to my questions: > > > > > > 1. Have I overlooked a fast way to test whether a GRanges object is > > sorted? > > > 2a. Could a is.unsorted,GenomicRanges-method be added to the > > > GenomicRanges package? Side note, I'm unsure at which level to define > > > this method, e.g., GRanges vs. GenomicRanges. > > > 2b. Is it possible to have a sensible definition and implementation > > > for is.unsorted,GRangesList-method? > > > 2c. Could a is.unsorted,RangedSummarizedExperiment-method be added to > > > the SummarizedExperiment package? > > > > > > I started working on a patch for 2a/2c, but wanted to ensure I hadn't > > > overlooked something obvious. Also, I'm sure 2a/2b/2c could be written > > > much more efficiently at the C-level but I'm afraid this might be a > > > bit beyond my abilities to integrate nicely with the existing code. > > > > > > Thanks, > > > Pete > > > > > > _______________________________________________ > > > 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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
