numLoops: Per-sample loop quantities

In diffloop: Identifying differential DNA loops from chromatin topology data

Description

numLoops counts number of loops for each sample based on the index of nloops and returns a data.frame

Usage

numLoops(dlo, nloops = 1:10)

## S4 method for signature 'loops,numeric'
numLoops(dlo, nloops = 1:10)

## S4 method for signature 'loops,missing'
numLoops(dlo, nloops = 1:10)

Arguments

dlo	A loops object
nloops	A numeric vector of counts to be considered

Details

This function shows the number of unique loops with at least nloops in counts. Can be used to quickly visualize relative sequencing depth between samples

Value

A data.frame

Examples

# Determine what samples have loops with 1-20 counts
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
nLoops <- numLoops(loops.small, 1:20)

# Determine what samples loops with 1-10 counts by default
nLoops <- numLoops(loops.small)

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