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

[Peter Hickey]

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