Hi, Subject says it all (I think), and I don't believe I've seen it reported before: R> library(GenomicRanges) R> gr <- GRanges(seqnames='chr1', IRanges(1:5, width=10), strand='+') R> gr[strand(gr) == '+'] Error in .IRanges.checkAndTranslateSingleBracketSubscript(x, i) : invalid subscript type R> gr2 <- gr R> strand(gr2)[5] <- '-' R> gr2[strand(gr2) == '+'] GRanges with 4 ranges and 0 elementMetadata values seqnames ranges strand | <rle> <iranges> <rle> | [1] chr1 [1, 10] + | [2] chr1 [2, 11] + | [3] chr1 [3, 12] + | [4] chr1 [4, 13] + | R> gr[Rle(rep(TRUE, 5))] Error in .IRanges.checkAndTranslateSingleBracketSubscript(x, i) : invalid subscript type R> gr[Rle(c(rep(TRUE, 4), F))] GRanges with 4 ranges and 0 elementMetadata values seqnames ranges strand | <rle> <iranges> <rle> | [1] chr1 [1, 10] + | [2] chr1 [2, 11] + | [3] chr1 [3, 12] + | [4] chr1 [4, 13] + | sessionInfo() R version 2.13.0 Under development (unstable) (2010-09-20 r52948) Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicRanges_1.1.25 IRanges_1.7.37 -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

On 09/29/2010 05:16 PM, Steve Lianoglou wrote: > Hi, > > Subject says it all (I think), and I don't believe I've seen it reported before: > > R> library(GenomicRanges) > R> gr <- GRanges(seqnames='chr1', IRanges(1:5, width=10), strand='+') > R> gr[strand(gr) == '+'] > Error in .IRanges.checkAndTranslateSingleBracketSubscript(x, i) : > invalid subscript type Thanks, fixed in 1.1.31. Martin > R> gr2 <- gr > R> strand(gr2)[5] <- '-' > R> gr2[strand(gr2) == '+'] > GRanges with 4 ranges and 0 elementMetadata values > seqnames ranges strand | > <rle> <iranges> <rle> | > [1] chr1 [1, 10] + | > [2] chr1 [2, 11] + | > [3] chr1 [3, 12] + | > [4] chr1 [4, 13] + | > > > R> gr[Rle(rep(TRUE, 5))] > Error in .IRanges.checkAndTranslateSingleBracketSubscript(x, i) : > invalid subscript type > > R> gr[Rle(c(rep(TRUE, 4), F))] > GRanges with 4 ranges and 0 elementMetadata values > seqnames ranges strand | > <rle> <iranges> <rle> | > [1] chr1 [1, 10] + | > [2] chr1 [2, 11] + | > [3] chr1 [3, 12] + | > [4] chr1 [4, 13] + | > > sessionInfo() > R version 2.13.0 Under development (unstable) (2010-09-20 r52948) > Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicRanges_1.1.25 IRanges_1.7.37 >