enrichDiffLogoObjectWithPvalues: Enriches a difflogo object with p-values

In DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

Description

Enriches a difflogo object with p-values which quantifies the probability that two PWM-positions are from the same distribution

Usage

enrichDiffLogoObjectWithPvalues(diffLogoObj, n1, n2,
  stackHeight = shannonDivergence, numberOfPermutations = 100)

Arguments

diffLogoObj	matrix of difflogo objects
n1	the number of sequences behind the first pwm behind the given difflogo object
n2	the number of sequences behind the second pwm behind the given difflogo object
stackHeight	function for the calculation of a divergence measure for two probability vectors
numberOfPermutations	the number of permutations to perform for the calculation of stackHeights

Value

enriched 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,".pwm",sep="")
  file = system.file(fileName, package = "DiffLogo")
  motifs[[name]] = getPwmFromPwmFile(file)
}

pwm1 = motifs[[motif_names[[1]]]]
pwm2 = motifs[[motif_names[[2]]]]
n1 <- 100
n2 <- 100
diffLogoObj = createDiffLogoObject(pwm1 = pwm1, pwm2 = pwm2)
diffLogoObj = enrichDiffLogoObjectWithPvalues(diffLogoObj, n1, n2)

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