| 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);