sortPerGroup: Sort a GRangesList

In JokingHero/ORFik: Open Reading Frames in Genomics

Sort a GRangesList

Description

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.

Usage

sortPerGroup(grl, ignore.strand = FALSE, quick.rev = FALSE)

Arguments

grl	a GRangesList
ignore.strand	a boolean, (default FALSE): should minus strands be sorted from highest to lowest ends. If TRUE: from lowest to highest ends.
quick.rev	default: FALSE, if TRUE, given that you know all ranges are sorted from min to max for both strands, it will only reverse coordinates for minus strand groups, and only if they are in increasing order. Much quicker

Details

Note: will not work if groups have equal names.

Value

an equally named GRangesList, where each group is sorted within group.

Examples

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)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.