enrichDiffLogoObjectWithPvalues {DiffLogo} | R Documentation |
Enriches a difflogo object with p-values which quantifies the probability that two PWM-positions are from the same distribution
enrichDiffLogoObjectWithPvalues(diffLogoObj, n1, n2, stackHeight = shannonDivergence, numberOfPermutations = 100)
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 |
enriched difflogo object
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)