makePWMPvalCutoffBackground {PWMEnrich} | R Documentation

## Construct a cutoff background from empirical background

### Description

This function takes already calculated empirical background distribution and chooses cutoff for each motif based on P-value cutoff for individual sites.

### Usage

    makePWMPvalCutoffBackground(bg.p, p.value = 0.001, bg.source = "")

### Arguments

`bg.p` | an object of class PWMEmpiricalBackground
`p.value` | the P-value used to find cuttoffs for each of the motifs
`bg.source` | textual description of background source

### Value

an object of type PWMCutoffBackground

### Examples

    ## Not run:
    if(requireNamespace("PWMEnrich.Dmelanogaster.background")){
       data(MotifDb.Dmel.PFM, package = "PWMEnrich.Dmelanogaster.background")

       # make empirical background - here we use only 100 sequences for illustrative purposes
    	  if(requireNamespace("BSgenome.Dmelanogaster.UCSC.dm3"))
         bg.p = makePWMEmpiricalBackground(Dmelanogaster$upstream2000[1:100], MotifDb.Dmel.PFM)

       # use the empirical background to pick a threshold and make cutoff background
       makePWMPvalCutoffBackground(bg.p, 0.001)
    }

    ## End(Not run)

[Package PWMEnrich version 4.28.1 Index]