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(require("PWMEnrich.Dmelanogaster.background")){
        data(MotifDb.Dmel)
        data(MotifDb.Dmel.PFM)

        # 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 4.16.0 Index]