diffloop (version 1.0.2)

filterLoops: Filter loops

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)
## S3 method for class '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

Value

• A loops object

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.

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)