Hi,
@Pete:
2a- I would just compare pairs of adjacent elements, taking
advantage of the fact that <= is vectorized and cheap. So something
like:
setMethod("is.unsorted", "Vector",
function(x, na.rm=FALSE, strictly=FALSE)
{
if (length(x) <= 1L)
return(FALSE)
x1 <- head(x, n=-1)
x2 <- tail(x, n=-1)
if (strictly)
return(any(x1 >= x2))
any(x1 > x2)
}
)
Since this will work on any Vector derivative for which <= and
subsetting are defined, it's a good candidate for being the default
"is.unsorted" method for Vector objects. I'll add it to S4Vectors.
2b- The semantic of is.unsorted() on a GRangesList object or any
List object in general should be sapply(x, is.unsorted), for
consistency with order(), sort(), etc:
> sort(IntegerList(4:3, 1:-2))
IntegerList of length 2
[[1]] 3 4
[[2]] -2 -1 0 1
I'll add this too.
2c - That won't be needed. The default method for Vector objects will
work on RangedSummarizedExperiment objects (<= and 1D subsetting are
defined and along the same dimension).
@Gabe:
See ?`GenomicRanges-comparison` for how the order of genomic ranges
is defined.
@Michael:
Calling base::.gt() in a loop sounds indeed very inefficient. What
about having base::is.unsorted() do the above on "objects" instead?
base::.gt() seems to also require that the object is subsettable so
the requirements are the same.
Then we wouldn't need the default "is.unsorted" method for Vector
objects, only a default "anyNA" method for Vector objects that always
returns FALSE (plus some specific ones for Rle and other Vector
derivatives that support NAs).
Thanks,
H.
On 11/02/2015 05:35 PM, Michael Lawrence 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
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Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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