topLoops {diffloop} | R Documentation

## Grab top loops

### 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)

[Package diffloop version 1.12.0 Index]