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(require("PWMEnrich.Dmelanogaster.background")){
   data(MotifDb.Dmel.PFM)

   # make empirical background - here we use only 100 sequences for illustrative purposes
	  if(require("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 4.16.0 Index]