2011/2/1 Hervé Pagès <hpages@fhcrc.org>

> Hi,
>
>
> On 02/01/2011 11:08 AM, Michael Lawrence wrote:
> [...]
>
>  This is a reasonable request. As Kasper mentioned, it's possible with post
>> processing.
>>
>> E.g.:
>>
>> m<- findOverlaps(query, subject)
>> percentOverlap<- width(ranges(m, query, subject)) /
>> width(query)[queryHits(m)]
>> keep<- percentOverlap>  cutoff
>>
>> Perhaps someone up North could add this to IRanges/GenomicRanges?
>>
>
> Would be my pleasure. Yes the functionality provided by this
> ranges,RangesMatching method is very useful but maybe we should try
> to give it a little bit more exposure. Right now it's kind of "hidden"
> in the man page for RangesMatching (which you will get with something
> like ?`RangesMatching-class` or ?`ranges,RangesMatching-method`) and
> not mentioned in any vignette AFAIK. Also it works only if query and
> subject are both Ranges objects but not with GRanges objects.
>
> So I propose to:
>
>  1. Rename this to something like overlaps(), or overlappingRanges(),
>     or ... (fill the blank), and deprecate the ranges,RangesMatching
>     method.
>     overlaps() would be a new generic with the m,query,subject
>     signature.
>     The current name is probably part of the reason why nobody (except
>     the original author of the method) knew about it.
>     I personally find it unexpected that a quite non-specific name
>     like "ranges" is used for this when it generally plays the role
>     of an accessor to get/set the ranges of containers like IRanges,
>     RangedData, GRanges, etc...
>
>  2. Add a "overlaps" method for
>     RangesMatching,GenomicRanges,GenomicRanges.
>
>  3. Illustrate how to use this in the vignettes of GenomicRanges.
>
> Would that be OK?
>
>
That would be great, but I was really referring to supporting a fractional
minOverlaps parameter to findOverlaps, etc. Sorry that I wasn't clear.


> H.
>
>
>> Michael
>>
>> D.
>>
>>>
>>>
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>>
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>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
>
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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