toPWM: Convert motifs into PWMs

In PWMEnrich: PWM enrichment analysis

Description

Convert motifs into PWMs

Usage

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),
  ...
)

Arguments

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

Examples

## 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)

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