topLoops: Grab top loops

Description Usage Arguments Details Value Examples

View source: R/assoc.R

Description

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

Usage

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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

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# 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)

Bioconductor-mirror/diffloop documentation built on June 1, 2017, 7:35 a.m.