makePWMPvalCutoffBackground: Construct a cutoff background from empirical background

In PWMEnrich: PWM enrichment analysis

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)

PWMEnrich documentation built on Nov. 8, 2020, 7:45 p.m.