topLoops: Grab top loops

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

Description

topLoops takes a loops object and performs basic filtering for FDR or PValue

Usage

topLoops(dlo, FDR, PValue)

## S4 method for signature 'loops,numeric,numeric'
topLoops(dlo, FDR, PValue)

## S4 method for signature 'loops,numeric,missing'
topLoops(dlo, FDR, PValue)

## S4 method for signature 'loops,missing,numeric'
topLoops(dlo, FDR, PValue)

Arguments

dlo	A loops object
FDR	Maximum threshold for False Discovery Rate; default = 1
PValue	Maximum threshold for P-value; default = 1

Details

This function returns a subsetted loops object where all loops meet the significance threshold specificed by the parameters in the function call.

Value

A loops object subsetted by specified parameters

Examples

# Differential loop calling between naive and primed
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
np <- loops.small[,1:4]
assoc_np <- quickAssoc(np)
top_np <- topLoops(assoc_np, FDR = 0.3)

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