PWMEnrich (version 4.8.2)

PFMtoPWM: 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
}