[Bioc-sig-seq] findOverlaps Documented Option

[Martin Morgan]

  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.

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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