PWMUnscaled: Create a PWM from PFM
In PWMEnrich: PWM enrichment analysis

Description Usage Arguments Details Value Examples

The PWM function from Biostrings without unit scaling

PWMUnscaled(
  x,
  id = "",
  name = "",
  type = c("log2probratio", "prob"),
  prior.params = c(A = 0.25, C = 0.25, G = 0.25, T = 0.25),
  pseudo.count = prior.params,
  unit.scale = FALSE,
  seq.count = NULL
)

`x`	the integer count matrix representing the motif, rows as nucleotides
`id`	a systematic ID given to this PWM, could include the source, version, etc
`name`	the name of the transcription factor (TF) to which the PWM corresponds to
`type`	the type of PWM calculation, either as log2-odds, or posterior probability (frequency matrix)
`prior.params`	the pseudocounts for each of the nucleotides
`pseudo.count`	the pseudo-count values if different from priors
`unit.scale`	if to unit.scale the pwm (default is no unit scaling)
`seq.count`	if x is a normalised PFM (i.e. with probabilities instead of sequence counts), then this sequence count will be used to convert `x` into a count matrix

By default the Biostrings package scales the log-odds score so it is within 0 and 1. In this function we take a more traditional approach with no unit scaling and offer unit scaling as an additional parameter.

See ?PWM from Biostrings for more information on input arguments.

a new PWM object representing the PWM

if(requireNamespace("PWMEnrich.Dmelanogaster.background")){
   data(MotifDb.Dmel.PFM, package = "PWMEnrich.Dmelanogaster.background")

   ttk = MotifDb.Dmel.PFM[["ttk"]]
   
   # make a PWM with uniform background
   PWMUnscaled(ttk, id="ttk-JASPAR", name="ttk")
   
   # custom background
   PWMUnscaled(ttk, id="ttk-JASPAR", name="ttk", 
     prior.params=c("A"= 0.2, "C" = 0.3, "G" = 0.3, "T" = 0.2))

   # get background for drosophila (quick mode on a reduced dataset)
   prior = getBackgroundFrequencies("dm3", quick=TRUE)
   
   # convert using genomic background
   PWMUnscaled(ttk, id="ttk-JASPAR", name="ttk", prior.params=prior)
}