padGRanges: Pad a GRanges object

In diffloop: Identifying differential DNA loops from chromatin topology data

Description

padGRanges takes a GRanges object and adds or substracts distance based on user-defined input. Upstream and downstream consider strand information when available. Specify only either pad or upstream/downstream when using

Usage

padGRanges(gro, upstream = 0, downstream = 0, pad = 0)

## S4 method for signature 'GRanges'
padGRanges(gro, upstream = 0, downstream = 0, pad = 0)

Arguments

gro	A granges object
upstream	Distance in BP added upstream
downstream	Distance in BP added downstream
pad	Distance in BP added

Value

A GRanges object with adjusted start and end values

Examples

#Read in CTCF Jurkat peaks in
ctcf_j <- system.file('extdata','Jurkat_CTCF_chr1.narrowPeak',package = 'diffloop')
ctcf <- bedToGRanges(ctcf_j)
ctcf.pad <- padGRanges(ctcf, pad = 1000)

diffloop documentation built on Nov. 8, 2020, 5:48 p.m.