filterLoops: Filter loops

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

Description

filterLoops filters out loops that aren't wide, aren't prevalent within samples or prevalent between samples

Usage

filterLoops(dlo, width = 0, nreplicates = 0, nsamples = 1)

## S4 method for signature 'ANY'
filterLoops(dlo, width = 0, nreplicates = 0, nsamples = 1)

Arguments

dlo	A loops object
width	Minimum loop width
nreplicates	Minimum number of counts per loop
nsamples	Minimum number of samples per loop per counts

Details

Function that restricts loops in a loops object. width specifies the minimum width between anchors. Default is zero. nreplicates restricts loops to at least this specified amount of counts is present in at least one sample. Instead of nreplicates being present in only one sample, nsamples specifies how many individual samples that a loop must have nreplicates in to be included after filtering.

Value

A loops object

Examples

rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
# Restrict loops to > 5kb width
filtered.jpn1 <- filterLoops(loops.small, 5000, 0, 0)
# Restrict loops to > 5kb width and have >= 3 replicates in >= 1 sample
filtered.jpn2 <- filterLoops(loops.small, 5000, 3, 1)
# Restrict loops to > 10kb width and have >= 3 replicates in >= 2 samples
filtered.jpn3 <- filterLoops(loops.small, 10000, 3, 2)

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