[Bioc-sig-seq] findOverlaps Documented Option

[Dario Strbenac]

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.

> 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