sortPerGroup {ORFik} | R Documentation |
A faster, more versatile reimplementation of
sort.GenomicRanges
for GRangesList,
needed since the original works poorly for more than 10k groups.
This function sorts each group, where "+" strands are
increasing by starts and "-" strands are decreasing by ends.
sortPerGroup(grl, ignore.strand = FALSE)
grl |
|
ignore.strand |
a boolean, if FALSE: should minus strands be sorted from highest to lowest ends. If TRUE: from lowest to highest ends. |
Note: will not work if groups have equal names.
an equally named GRangesList, where each group is sorted within group.
gr_plus <- GRanges(seqnames = c("chr1", "chr1"), ranges = IRanges(c(14, 7), width = 3), strand = c("+", "+")) gr_minus <- GRanges(seqnames = c("chr2", "chr2"), ranges = IRanges(c(1, 4), c(3, 9)), strand = c("-", "-")) grl <- GRangesList(tx1 = gr_plus, tx2 = gr_minus) sortPerGroup(grl)