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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