On Mon, Aug 23, 2010 at 2:49 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

>  On 8/22/2010 5:30 PM, Dario Strbenac wrote:
>
>> Hi again,
>>
>> I'm just trying my alternate way to get maximum overlaps, and I've now
>> made a small and simple example to show that minoverlap seems to be
>> unimplemented, since I get a warning message about it being ignored.
>>
>
> Hi Dario -- as a partial response, I'll just note that this is documented.
> The help pages for S4 methods can be tricky to find. I did
>
> > showMethods(findOverlaps)
> Function: findOverlaps (package IRanges)
> [snip]
> query="GRanges", subject="GRanges"
>
> > ?"findOverlaps,GRanges,GRanges-method"
>
> and saw
>
> Arguments:
> [snip]
> minoverlap: Ignored.
>
> I don't know why minoverlap is ignored for this combination of data
> objects; it could be that the semantics are subtly inconsistent (likely
> reason) or that the authors have just not had a pressing need to implement
> this. It does suggest a bit of a tortuous work-around, though, which is to
> extract the ranges() from your GRanges objects and perform findOverlaps on
> those. You'll of course have to manage the sequence and strand data
> yourself.
>
>
If you ignore the strand, you could use a RangesList:

rl <- as(granges, "RangesList")

Or you can do the minoverlap filtering yourself from the matching result
using pintersect to find the overlapping region and then filtering on the
width.


Martin
>
>
>  gr<- GRanges(seqnames = Rle(c("chr1", "chr2", "chr1",
>>>
>> + "chr3"), c(1, 3, 2, 4)), ranges = IRanges(1:10, end = 7:16,
>> + names = head(letters, 10)), strand = Rle(strand(c("-",
>> + "+", "*", "+", "-")), c(1, 2, 2, 3, 2)), score = 1:10,
>> + GC = seq(1, 0, length = 10))
>>
>>> gr2<- GRanges(seqnames = c("chr1", "chr1"), ranges = IRanges(c(7,
>>>
>> + 13), width = 3), strand = c("+", "-"), score = 3:4,
>> + GC = c(0.3, 0.5))
>>
>>> findOverlaps(gr, gr2, minoverlap = 9)
>>>
>> An object of class "RangesMatching"
>> Slot "matchMatrix":
>>      query subject
>> [1,]     5       1
>> [2,]     6       1
>>
>> Slot "DIM":
>> [1] 10  2
>>
>> Warning message:
>> In .local(query, subject, maxgap, minoverlap, type, select, ...) :
>>   'minoverlap' argument is ignored
>>
>>> sessionInfo()
>>>
>> R version 2.11.0 (2010-04-22)
>> x86_64-pc-mingw32
>>
>> locale:
>> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
>>  LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
>> [5] LC_TIME=English_Australia.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] GenomicRanges_1.0.7 IRanges_1.6.15
>>
>> --------------------------------------
>> Dario Strbenac
>> Research Assistant
>> Cancer Epigenetics
>> Garvan Institute of Medical Research
>> Darlinghurst NSW 2010
>> Australia
>>
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>>
>
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