Hi there, Is findOverlaps supposed to work on GRanges objects? For me it works on RangedData but not on GRanges - see below for the error, sessionInfo, etc. It would be useful for me if it could also work on GRanges, so if this doesn't count as a bug report can we count it as a feature request?
thanks very much, Janet ------------------------------------------------------------------- Dr. Janet Young (Trask lab) Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., C3-168, P.O. Box 19024, Seattle, WA 98109-1024, USA. tel: (206) 667 1471 fax: (206) 667 6524 email: jayoung ...at... fhcrc.org http://www.fhcrc.org/labs/trask/ ------------------------------------------------------------------- > library(GenomicRanges) Loading required package: IRanges Attaching package: 'IRanges' The following object(s) are masked from 'package:base': cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, table > > myregions_GR <- > GRanges(seqnames=c("chr1","chr1","chr2"),ranges=IRanges(start=c(101L,201L,101L),end=c(250L,301L,201L)) > ) > > findOverlaps(myregions_GR) Error in match.arg(type) : 'arg' must be of length 1 > > > myregions_RD <- > RangedData(IRanges(start=c(101L,201L,101L),end=c(250L,301L,201L)),space=c("chr1","chr1","chr2"),strand=c("+","+","+") > ) > > findOverlaps(myregions_RD) RangesMatchingList of length 2 names(2): chr1 chr2 > > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicRanges_1.2.3 IRanges_1.8.9 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
