prepareDiffLogoTable {DiffLogo} | R Documentation |
Prepares a DiffLogoTable and generates an object that contains the hirarchical clustering and a matrix of prepared difference logos.
prepareDiffLogoTable(PWMs, alphabet = DNA, configuration = list())
PWMs |
a list/vector of position weight matrices (PWMs) each of type pwm, data.frame, or matrix |
alphabet |
the alphabet of the given PWMs |
configuration |
list of (probably part of) of configuration options. See diffLogoTableConfiguration. |
matrix of difference logos
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) diffLogoTableObj = prepareDiffLogoTable(motifs);