PFMtoPWM {PWMEnrich} | R Documentation

## Convert frequencies into motifs using PWMUnscaled

### Description

Convert frequencies into motifs using PWMUnscaled

### 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

    if(require("PWMEnrich.Dmelanogaster.background")){
       data(MotifDb.Dmel.PFM)

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

       prior = getBackgroundFrequencies("dm3", quick=TRUE) # get background for drosophila (quick mode on a reduced dataset)
       PFMtoPWM(MotifDb.Dmel.PFM, prior.params=prior) # convert with genomic background
    }

[Package PWMEnrich version 4.16.0 Index]