Hi, When I use big set of GrangesList, I found it become very slow when metadata contain AtomicList. e.g.
> grll <- GRanges(seqnames="chr1", ranges=IRanges(start=1:500, width=2), > someInfo=rep(RleList("*"), 500)) > grr <- split(grll, 1:500) > grl <- as.list(grr) > system.time(grl<- grl[500:1]) user system elapsed 0 0 0 > system.time(grr<- grr[500:1]) user system elapsed 1.622 0.013 1.635 > grll <- GRanges(seqnames="chr1", ranges=IRanges(start=1:500, width=2)) > grr <- split(grll, 1:500) > grl <- as.list(grr) > system.time(grl<- grl[500:1]) user system elapsed 0 0 0 > system.time(grr<- grr[500:1]) user system elapsed 0.029 0.001 0.030 > sessionInfo() R Under development (unstable) (2013-07-23 r63392) Platform: x86_64-apple-darwin12.4.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicRanges_1.13.36 XVector_0.1.0 IRanges_1.19.24 BiocGenerics_0.7.3 loaded via a namespace (and not attached): [1] stats4_3.1.0 tools_3.1.0 Is there any method to improve this? Yours sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel