shannonDivergence {DiffLogo} | R Documentation

## shannon divergence

### Description

the shannon divergence for the given pair of probability vectors

### Usage

    shannonDivergence(p1, p2)

### Arguments

`p1` | probability vector representing the first symbol distribution
`p2` | probability vector representing the second symbol distribution

### Value

an object consisting of height and ylab

### Author(s)

Martin Nettling

### Examples

    motif_folder= "extdata/pwm"
    motif_names = c("HepG2","MCF7","HUVEC","ProgFib")
    motifs = list()
    for (name in motif_names) {
      fileName = paste(motif_folder,"/",name,".pwm",sep="")
      file = system.file(fileName, package = "DiffLogo")
      motifs[[name]] = getPwmFromPwmFile(file)
    }

    pwm1 = motifs[[motif_names[[1]]]]
    pwm2 = motifs[[motif_names[[2]]]]

    diffLogoFromPwm(pwm1 = pwm1, pwm2 = pwm2, stackHeight = shannonDivergence)

[Package DiffLogo version 2.8.0 Index]