diffloop (version 1.0.2)

topLoops: Grab top loops

Description

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

Usage

topLoops(dlo, FDR, PValue)
## S3 method for class 'loops,numeric,numeric':
topLoops(dlo, FDR, PValue)
## S3 method for class 'loops,numeric,missing':
topLoops(dlo, FDR, PValue)
## S3 method for class '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

Value

• A loops object subsetted by specified parameters

Details

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

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)