stitchRanges: Stitch Ranges within a given distance

In steveped/extraChIPs: Additional functions for working with ChIP-Seq data

Stitch Ranges within a given distance

Description

Stitch together ranges within a given distance, using excluded ranges as barriers that cannot be crossed

Usage

stitchRanges(x, exclude, maxgap = 12500L, ignore.strand = TRUE)

Arguments

x	Ranges to be stitched together
exclude	Ranges to exclude
maxgap	The maximum distance between ranges to be stitched
ignore.strand	logical

Details

Stitches together ranges within a given distance, using any ranges provided for exclusion as barriers between stitched ranges. This may be particularly useful if wanting to stitch enhancers whilst excluding promoters.

All inputs and outputs are Genomic Ranges objects

Value

A GRanges object

Examples

x <- GRanges(c("chr1:1-10", "chr1:101-110", "chr1:201-210", "chr2:1-10"))
y <- GRanges("chr1:200:+")
stitchRanges(x, exclude = y, maxgap = 100)

steveped/extraChIPs documentation built on Aug. 1, 2024, 12:36 a.m.