DiffLogo (version 1.2.1)

shannonDivergence: 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

Examples

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

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

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