motifIC {PWMEnrich}

R Documentation

Information content for a PWM or PFM

Description

Information content for a PWM or PFM

Usage

motifIC(
  motif,
  prior.params = c(A = 0.25, C = 0.25, G = 0.25, T = 0.25),
  bycol = FALSE
)

Arguments

motif	a matrix of frequencies, or a PWM object
prior.params	the prior parameters to use when a matrix is given (ignored if motif is already a PWM)
bycol	if to return values separately for each column

Value

information content in bits (i.e. log2)

Examples

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

   # the nucleotide distribution is taken from the PWM (in this case genomic background)
   motifIC(MotifDb.Dmel[["ttk"]]) 
   # information content with default uniform background because the input is a matrix, 
   # not PWM object
   motifIC(MotifDb.Dmel.PFM[["ttk"]]) 
}

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