Clonality-package       Clonality testing
ECMtesting              Clonality testing of >=3 tumors using Extended
                        Concordant Mutations (ECM) test based on LOH
                        (Loss of Heterozygosity) profiles
LOHclonality            Clonality testing using LOH (Loss of
                        Heterozygosity) profiles
LRtesting3or4tumors     Clonality testing of 3 or 4 tumors using
                        Likelihood model based on LOH (Loss of
                        Heterozygosity) profiles
ave.adj.probes          Averaging of adjacent probes in copy number
                        arrays
chromosomePlots         Per-chromosome plots of the copy number arrays
                        from a particular patient
clonality.analysis      Clonality testing using copy number data
genomewidePlots         Plot of the genomewide copy number profiles of
                        a pair of tumors.
histogramPlot           Histrograms of Log-Likelihood Ratios
splitChromosomes        Chromosome splitting
