DiffLogo (version 1.2.1)

createDiffLogoObject: DiffLogo object

Description

Creates a DiffLogo object

Usage

createDiffLogoObject(pwm1, pwm2, stackHeight = shannonDivergence, baseDistribution = normalizedDifferenceOfProbabilities, alphabet = DNA)

Arguments

pwm1

representation of the first position weight matrix (PWM) of type pwm, data.frame, or matrix

pwm2

representation of the second position weight matrix (PWM) of type pwm, data.frame, or matrix

stackHeight

function for the height of a stack at position i

baseDistribution

function for the heights of the individual bases

alphabet

of type Alphabet

Value

DiffLogo object

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]]]]

diffLogoObj = createDiffLogoObject(pwm1 = pwm1, pwm2 = pwm2)
diffLogo(diffLogoObj)