toPWM {PWMEnrich} | R Documentation |
Convert motifs into PWMs
toPWM( motifs, ids = names(motifs), targets = names(motifs), seq.count = 50, prior = c(A = 0.25, C = 0.25, G = 0.25, T = 0.25), ... )
motifs |
a list of motifs either as position probability matrices (PPM) or frequency matirces (PFMs) |
ids |
the set of IDs for the motifs (defaults to names of the 'motifs' list) |
targets |
the set of target TF names for the motifs (defaults to names of the 'motifs' list) |
seq.count |
provides a vector of sequence counts for probability matrices (PPMs). Default it 50. |
prior |
frequencies of the four letters in the genome. Default is uniform background. |
... |
other parameters to PWMUnscaled |
## Not run: if (requireNamespace("PWMEnrich.Dmelanogaster.background")) { data(MotifDb.Dmel.PFM, package = "PWMEnrich.Dmelanogaster.background") toPWM(MotifDb.Dmel.PFM) # convert to PWM with uniform background # get background for drosophila (quick mode on a reduced dataset) prior = getBackgroundFrequencies("dm3", quick=TRUE) toPWM(MotifDb.Dmel.PFM, prior=prior) # convert with genomic background } ## End(Not run)