enrichDiffLogoTableWithPvalues {DiffLogo} | R Documentation |
Enriches a matrix of difflogo objects with p-values which quantifies the probability that two PWM-positions are from the same distribution
enrichDiffLogoTableWithPvalues(diffLogoObjMatrix, sampleSizes, stackHeight = shannonDivergence, numberOfPermutations = 100)
diffLogoObjMatrix |
matrix of difflogo objects |
sampleSizes |
number of sequences behind the pwms behind the given difflogo objects |
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 |
matrix of difflogo objects enriched with p-values
Martin Nettling
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) } sampleSizes <- c(100, 150, 200, 250) names(sampleSizes) <- motif_names diffLogoTableObj = prepareDiffLogoTable(motifs); diffLogoTableObj$diffLogoObjMatrix = enrichDiffLogoTableWithPvalues(diffLogoTableObj$diffLogoObjMatrix, sampleSizes)