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
SNVtest                 Testing relatedness (clonality) of two tumors
                        from the same patient using profiles of somatic
                        mutations
SNVtest2                Test for tumors from 2 different sites
ave.adj.probes          Averaging of adjacent probes in copy number
                        arrays
chromosomePlots         Per-chromosome plots of the copy number arrays
                        from a particular patient
clonEM                  Auxiliary EM algorithm Function.
clonality.analysis      Clonality testing using copy number data
create.mutation.matrix
                        Formatting matrix of mutations
freqdata                TCGA pancancer mutation frequencies
genomewidePlots         Plot of the genomewide copy number profiles of
                        a pair of tumors.
get.mutation.frequencies
                        Estimating mutation frequencies based on the
                        TCGA data or a submitted reference mutations
                        file
grid.lik                Auxiliary function: Grid of conditional
                        probabilities
histogramPlot           Histrograms of Log-Likelihood Ratios
lcis                    Breast cancer data
model.lik               Auxiliary likelihood Function
mutation.proba          Probability of being clonal
mutation.rem            Estimation of the random-effect model for
                        clonality based on mutations.
print.mutation.proba    Print for the mutation.proba function
print.mutation.rem      Print for the mutation.rem function
splitChromosomes        Chromosome splitting
xidens                  Auxiliary function computing the density of xi
