keepCTCFloops: Keep CTCF loops

In diffloop: Identifying differential DNA loops from chromatin topology data

Description

keepCTCFloops returns loops that are nearby CTCF peaks as determined by some external data in a GRanges object

Usage

keepCTCFloops(lto, ctcf)

## S4 method for signature 'loops,GRanges'
keepCTCFloops(lto, ctcf)

Arguments

lto	A loops object whose loops will be annotated
ctcf	GRanges object corresponding to locations of CTCF peaks

Details

This function works similar to the annotateLoops function but returns only CTCF loops that are defined in this function. However, loops in annotateLoops may have a different annotation based on their priority scheme. For example, an e-p loop from annotateLoops may be returned as a CTCF loop by this function if the loop had both annotations. These peaks don't necessarily need to be CTCF peaks, so using a GRanges object with enhancers or promoters to determine e-e loops and p-p loops could also be used in this function

Value

A loops object with all loops having both anchors in the GRanges region

Examples

rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
ctcf_j <- system.file('extdata','Jurkat_CTCF_chr1.narrowPeak',package='diffloop')
ctcf <- rmchr(padGRanges(bedToGRanges(ctcf_j), pad = 1000))
# small.ctcf <- keepCTCFloops(loops.small, ctcf)

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