[BioC] GRanges setdiff With Features on Both Strands

[Hervé Pagès]

OK, thanks everybody for their feedback. This is done in GenomicRanges
1.6.6 (release) and 1.7.16 (devel).

Summary: when called with 'ignore.strand=TRUE', the "range", "disjoin",
"reduce", "union", "intersect" and "setdiff" methods for GRanges or
GenomicRanges objects now behave like if they set the strand of the
input to "*" before they do any computation.

Cheers,
H.


On 01/23/2012 03:00 PM, Dario Strbenac wrote:
>> From a biological point of view, I would say the first form. This would happen in a situation like when you have have stranded reads and the other GRanges is a set of repeats locations, which are unstranded blocks in the genome. But the second form is mathematically sound. So, that would be the best form to choose.
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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