[Bioc-devel] %outside% on GRanges

James W. MacDonald jm@cdon @end|ng |rom uw@edu
Wed May 26 16:27:17 CEST 2021

Hi Oleksii,

That function is just a simplification of the negation of overlapsAny:

> getAnywhere("%outside%")
A single object matching '%outside%' was found
It was found in the following places
with value

function (query, subject) 
!overlapsAny(query, subject)
<bytecode: 0x00000000120f7218>
<environment: namespace:IRanges>

And overlapsAny has dispatch on Granges objects via inheritance from the Vector class.

> showMethods("overlapsAny")
Function: overlapsAny (package IRanges)
query="GRanges", subject="GRanges"
    (inherited from: query="Vector", subject="Vector")
query="integer", subject="Vector"
query="IntegerRangesList", subject="IntegerRangesList"
query="Vector", subject="missing"
query="Vector", subject="Vector"

So far as I can tell there is no code in GenomicRanges to make this happen - it just dispatches via inheritance - so there is no direct help page in GenomicRanges.



-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of Oleksii Nikolaienko
Sent: Wednesday, May 26, 2021 9:15 AM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] %outside% on GRanges

Dear Bioc team,
%outside% operator from IRanges works as one would expect even if GRanges objects are supplied as operands:

> a <- as("chr1:100-200", "GRanges")
> b <- as("chr2:150-250", "GRanges")
> IRanges::`%outside%`(a, b)
[1] TRUE

> IRanges::`%outside%`(ranges(a), ranges(b))

It is correct and intuitive, but %outside% does not seem to be defined or included in help pages of the GenomicRanges library. Can I rely on such behaviour of %outside% in the future?

Oleksii Nikolaienko

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