Hi Ivan, On Thu, Jul 8, 2010 at 11:48 AM, Ivan Gregoretti <[email protected]> wrote: > Can anybody show an example of how to sort GRanges by score? > > Lets say I have this GRanges instance > > library(GenomicRanges) > > gr <- GRanges(seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, > 3, 2, 4)), ranges = IRanges(1:10, end = 7:16, names = head(letters, > 10)), strand = Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, > 2)), score = 1:10, GC = seq(1, 0, length = 10)) > > gr > GRanges with 10 ranges and 2 elementMetadata values > seqnames ranges strand | score GC > <Rle> <IRanges> <Rle> | <integer> <numeric> > a chr1 [ 1, 7] - | 1 1.0000000 > b chr2 [ 2, 8] + | 2 0.8888889 > c chr2 [ 3, 9] + | 3 0.7777778 > d chr2 [ 4, 10] * | 4 0.6666667 > e chr1 [ 5, 11] * | 5 0.5555556 > f chr1 [ 6, 12] + | 6 0.4444444 > g chr3 [ 7, 13] + | 7 0.3333333 > h chr3 [ 8, 14] + | 8 0.2222222 > i chr3 [ 9, 15] - | 9 0.1111111 > j chr3 [10, 16] - | 10 0.0000000 > > seqlengths > chr1 chr2 chr3 > NA NA NA > > How do I re-order the rows in descending score values?
How about: R> o <- order(elementMetadata(gr)$score, decreasing=TRUE) R> gr <- gr[o] > How do I subset the top 3 score ranges? If you did the above move: R> gr[1:3] If you didn't reorder gr based on o, you could do: R> gr[o[1:3]] -- 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
