Entering edit mode
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