callCCDs: Compute Chromatin Contact Domains (CCDs)

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

Description

callCCDs determines regions

Usage

callCCDs(lo, petWeights = FALSE, lowCoveragePercentile = 0.05)

## S4 method for signature 'ANY'
callCCDs(lo, petWeights = FALSE,
  lowCoveragePercentile = 0.05)

Arguments

lo	A loops object
petWeights	Boolean to weight loop coverage by number of PETs. Default = FALSE
lowCoveragePercentile	Percentile of low coverage to be dropped. Default = 0.05

Details

This funciton returns a GRanges object of regions determined to be Chromatin Contact Domains as defined in the Tang et al. 2015 paper from the Ruan group. Users can choose to weight the loops by the total number PETs (across all samples) or not and what percent. For details of this method, see page 12 of the supplement of PMID:26686651. Make sure there are only loops within a chromosome before calling this.

Value

A GRanges object of called Chromatin Contact domains

Examples

rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
#lo <- subsetLoops(loops.small, c(1,2,5,6,7,8,9,27,69))
#ccd <- callCCDs(lo, petWeights = TRUE, lowCoveragePercentile = 0.5)

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