PFMtoPWM {PWMEnrich} | R Documentation

## Convert frequencies into motifs using PWMUnscaled

### Description

Note that this function is deprecated and replaced by `toPWM()`.

### Usage

    PFMtoPWM(
      motifs,
      id = names(motifs),
      name = names(motifs),
      seq.count = NULL,
      ...
    )

### Arguments

`motifs` | a list of motifs represented as matrices of frequencies (PFM)
`id` | the set of IDs for the motifs (defaults to names of the 'motifs' list)
`name` | the set of names for the motifs (defaults to names of the 'motifs' list)
`seq.count` | if frequencies in the motifs are normalized to 1, provides a vector of sequence counts (e.g. for MotifDb motifs)
`...` | other parameters to PWMUnscaled

### Examples

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

      # convert to PWM with uniform background
      PFMtoPWM(MotifDb.Dmel.PFM)

      # get background for drosophila (quick mode on a reduced dataset)
      prior = getBackgroundFrequencies("dm3", quick=TRUE)

      # convert with genomic background
      PFMtoPWM(MotifDb.Dmel.PFM, prior.params=prior)
    }

    ## End(Not run)

[Package PWMEnrich version 4.28.1 Index]