makePWMCutoffBackground {PWMEnrich}R Documentation

Make a cutoff background

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)

[Package PWMEnrich version 4.26.0 Index]