removeRegion: Remove region from loops object

In aryeelab/diffloop: Identifying differential DNA loops from chromatin topology data

Description

removeRegion takes a loops object and a GRanges object and returns a loops object where neither anchors map inside the GRanges coordinates.

Usage

removeRegion(dlo, region)

## S4 method for signature 'loops,GRanges'
removeRegion(dlo, region)

Arguments

dlo	A loops object to be subsetted
region	A GRanges object containing region of interest

Value

A loops object with no anchors touching the region given

Examples

# Remove region chr1:36000000-36100000
library(GenomicRanges)
regA <- GRanges(c('1'),IRanges(c(36000000),c(36100000)))
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
# Get rid of loop if either anchor touches that region
restricted <- removeRegion(loops.small, regA)

aryeelab/diffloop documentation built on May 12, 2019, 3:42 a.m.