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]