sortPerGroup {ORFik} | R Documentation

## 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)

### Arguments

`grl` | a `GRangesList`
`ignore.strand` | a boolean, if FALSE: should minus strands be sorted from highest to lowest ends. If TRUE: from lowest to highest ends.

### 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)

[Package ORFik version 1.4.1 Index]