| PFMtoPWM {PWMEnrich} | R Documentation |
Convert frequencies into motifs using PWMUnscaled
PFMtoPWM(motifs, id = names(motifs),
name = names(motifs), seq.count = NULL, ...)
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 |
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
}