[Bioc-devel] ignoreSelf Option for findOverlaps of GenomicRanges Query

[Hervé Pagès]

On 10/26/2016 06:21 AM, Michael Lawrence wrote:
> There is only one general method for this case, on Vector,missing, so
> it's consistent by definition. Note that ignoreSelf and
> ignoreRedundant are defunct (and maybe even removed now).

Yep, defunct in release. Just removed them now in devel (IRanges 2.9.1).

H.


> The new
> argument names are drop.self and drop.redundant.
>
> Michael
>
> On Wed, Oct 26, 2016 at 3:00 AM, Dario Strbenac
> <dstr7320 at uni.sydney.edu.au> wrote:
>> Good day,
>>
>> For an IRanges object, findOverlaps has ignoreSelf and ignoreRedundant options. However, these aren't available for a GenomicRanges input object, even though the subject parameter is optional and a query GRanges object can be overlapped with itself. Could this be changed to be consistent?
>>
>> --------------------------------------
>> Dario Strbenac
>> University of Sydney
>> Camperdown NSW 2050
>> Australia
>> _______________________________________________
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>
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-- 
Hervé Pagès

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