ranges-flank: Generate flanking regions

In sa-lee/plyranges: A fluent interface for manipulating GenomicRanges

Generate flanking regions

Description

Find flanking regions to the left or right or upstream or downstream of a Ranges object.

Usage

flank_left(x, width = 0L)

flank_right(x, width = 0L)

flank_upstream(x, width = 0L)

flank_downstream(x, width = 0L)

Arguments

x	a Ranges object.
width	the width of the flanking region relative to the ranges in x. Either an integer vector of length 1 or an integer vector the same length as x. The width can be negative in which case the flanking region is reversed.

Details

The function flank_left will create the flanking region to the left of starting coordinates in x, while flank_right will create the flanking region to the right of the starting coordinates in x. The function flank_upstream will flank_left if the strand of rows in x is not negative and will flank_right if the strand of rows in x is negative. The function flank_downstream will flank_right if the strand of rows in x is not negative and will flank_leftt if the strand of rows in x is negative.

By default flank_left and flank_right will ignore strandedness of any ranges, while flank_upstream and flank_downstream will take into account the strand of x.

Value

A Ranges object of same length as x.

See Also

IRanges::flank(), GenomicRanges::flank()

Examples

gr <- as_granges(data.frame(start = 10:15,
                            width = 5,
                            seqnames = "seq1",
                            strand = c("+", "+", "-", "-", "+", "*")))
flank_left(gr, width = 5L)
flank_right(gr, width = 5L)
flank_upstream(gr, width = 5L)
flank_downstream(gr, width = 5L)

sa-lee/plyranges documentation built on April 15, 2024, 12:25 p.m.