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 <[email protected]>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: [email protected] > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
