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) |
prior |
frequencies of the four letters in the genome. Default is uniform background |
... |
other parameters to PWMUnscaled |
if(require("PWMEnrich.Dmelanogaster.background")){ data(MotifDb.Dmel.PFM) toPWM(MotifDb.Dmel.PFM) # convert to PWM with uniform background prior = getBackgroundFrequencies("dm3", quick=TRUE) # get background for drosophila (quick mode on a reduced dataset) toPWM(MotifDb.Dmel.PFM, prior=prior) # convert with genomic background }