[Bioc-devel] is.unsorted method for GRanges objects

[Peter Haverty]

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.
phaverty at gene.com

On Mon, Nov 2, 2015 at 5:35 PM, Michael Lawrence <lawrence.michael at 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.gabe at 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.hickey at 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 at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> >
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