makePWMCutoffBackground: Make a cutoff background

In PWMEnrich: PWM enrichment analysis

Description

Make a background based on number of motifs hits above a certain threshold.

Usage

makePWMCutoffBackground(
  bg.seq,
  motifs,
  cutoff = log2(exp(4)),
  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.
cutoff	the cutoff at which the background should be made, i.e. at which a motif hit is called significant
bg.pseudo.count	the pseudo count which is shared between nucleotides when frequency matrices are given
bg.source	a free-form textual description of how the background was generated
verbose	if to produce verbose output

Examples

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

   # make background for MotifDb motifs using 2Kb promoters of all D. melanogaster transcripts 
   # using a cutoff of 5
	  if(requireNamespace("BSgenome.Dmelanogaster.UCSC.dm3")) 
     makePWMCutoffBackground(Dmelanogaster$upstream2000, MotifDb.Dmel.PFM, cutoff=log2(exp(5)))
}

## End(Not run)

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