I'm not really sure what I was thinking when I made the self-self
findOverlaps accept a RangesList. Anyway, it should work now in svn.

Michael

On Tue, Jul 6, 2010 at 4:50 AM, Aaron Statham <a.statham@garvan.org.au>wrote:

> Tested in both R 2.11 & R-devel (IRanges 1.7.7) - see below
>
> > library(IRanges)
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
>    cbind, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
>    rbind, rep.int, table
>
> > showMethods("matchMatrix")
> Function: matchMatrix (package IRanges)
> x="RangesMatching"
>
> > temp <- RangedData(IRanges(1:10, width=2),
> space=sample(c("chr1","chr2"),10, replace=TRUE))
> > temp
> RangedData with 10 rows and 0 value columns across 2 spaces
>         space    ranges |
>   <character> <IRanges> |
> 1         chr1  [ 1,  2] |
> 2         chr1  [ 4,  5] |
> 3         chr1  [ 5,  6] |
> 4         chr1  [ 6,  7] |
> 5         chr1  [ 7,  8] |
> 6         chr1  [ 8,  9] |
> 7         chr2  [ 2,  3] |
> 8         chr2  [ 3,  4] |
> 9         chr2  [ 9, 10] |
> 10        chr2  [10, 11] |
> > findOverlaps(temp)
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "matchMatrix", for
> signature "RangesMatchingList"
> > findOverlaps(temp, temp)
> RangesMatchingList of length 2
> names(2): chr1 chr2
> > sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] IRanges_1.6.8
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.0
>
> At the moment I'm working around it but it would be nice to be able to use
> the ignoreSelf options available when doing self-queries.
> Thanks,
> Aaron
>
> --
> Aaron Statham
> Postgraduate Scholar, Cancer Epigenetics
> Garvan Institute of Medical Research   Tel: (02) 9295 8393
> 384 Victoria St Darlinghurst 2010   Fax: (02) 9295 8316
> NSW Australia         email: a.statham@garvan.org.au
>
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>
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