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"]])
    }

[Package PWMEnrich version 4.28.1 Index]