minoverlap is the number of bases in the query range that must overlap with
the subject range in order for it to be considered an overlap.  for example

foo = GRanges( c('chr1','chr1','chr1'),
                IRanges( start=c(1, 5, 10),
                           end=c(10,10,10) ),
                strand='*')
bar = GRanges( c('chr1'),
                IRanges( start=1, end=10 ),
                strand='*' )

show(foo)
show(bar)

findOverlaps(foo, bar, minoverlap=5)

or perhaps more illustratively,

subsetByOverlaps(foo, bar, minoverlap=1)
subsetByOverlaps(foo, bar, minoverlap=5)
subsetByOverlaps(foo, bar, minoverlap=10)

Does this make sense?  I didn't cover gapping, but Herve can answer that
1000x better than I can.


On Tue, Jun 5, 2012 at 1:11 PM, Kurinji Pandiyan <kurinji.pandiyan@gmail.com
> wrote:

> Hello,
>
> I am new to using the Genomic Ranges package and manipulating GRanges
> objects but I am currently attempting to overlap two GRanges objects. This
> is the command I used -
>
> findOverlaps(duke.dnase, h1.midmethgr, maxgap = 0L, minoverlap = 1L,type =
> "any", select ="all")
>
> where - duke.dnase and h1.midmethgr are the two GRanges objects.
>
> I am wondering how to play with the parameters in order to perform a more
> stringent overlap - I would like to modify with the number of base pairs
> that need to overlap between coordinates in order for it to be considered a
> hit. I am unsure as to what mioverlap = 1L means for this purpose.
>
> I would really appreciate your help.
>
> Thank you,
> Kurinji
>
> Graduate Student
> Johns Hopkins University/University of Southern California
>
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>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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