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: [email protected]
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