PFMtoPWM: Convert frequencies into motifs using PWMUnscaled

In PWMEnrich: PWM enrichment analysis

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)

PWMEnrich documentation built on Nov. 8, 2020, 7:45 p.m.