makePWMPvalCutoffBackgroundFromSeq {PWMEnrich} | R Documentation

## Construct a P-value cutoff background from a set of sequences

### 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)

[Package PWMEnrich version 4.28.1 Index]