makePWMPvalCutoffBackgroundFromSeq: Construct a P-value cutoff background from a set of sequences

In PWMEnrich: PWM enrichment analysis

Description

This function creates a P-value cutoff background for motif enrichment.

Usage

makePWMPvalCutoffBackgroundFromSeq(
  bg.seq,
  motifs,
  p.value = 0.001,
  bg.pseudo.count = 1,
  bg.source = "",
  verbose = TRUE
)

Arguments

bg.seq	a set of background sequences, either a list of DNAString object or DNAStringSet object
motifs	a set of motifs, either a list of frequency matrices, or a list of PWM objects. If frequency matrices are given, the background distribution is fitted from bg.seq.
p.value	the P-value used to find cuttoffs for each of the motifs
bg.pseudo.count	the pseudo count which is shared between nucleotides when frequency matrices are given
bg.source	textual description of background source
verbose	if to print verbose output

Value

an object of type PWMCutoffBackground

Examples

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

   # use the empirical background to pick a threshold and make cutoff background
   makePWMPvalCutoffBackground(Dmelanogaster$upstream2000, 0.001)
}

## End(Not run)

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