normalizedDifferenceOfProbabilities: normalized probability differences

In DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

Description

probability differences normalized by the sum of absolute probability differences for the given pair of probability vectors

Usage

normalizedDifferenceOfProbabilities(p1, p2)

Arguments

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

Value

a vector with one result for each symbol

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, baseDistribution = normalizedDifferenceOfProbabilities)

DiffLogo documentation built on Nov. 8, 2020, 6:09 p.m.