assignMutations         Mutation Assignment
assignQuantityToMutation
                        Quantity assignment (copy number) to mutations
assignQuantityToSP      Quantity assignment (ploidy) to subpopulations
buildMultiSamplePhylo   Relations between inter- and intra-sample
                        subpopulations
buildPhylo              Relations between subpopulations
cbs                     Matrix of copy number fragments
cellfrequency_pdf       Computes the probability distribution of
                        cellular frequencies for a single mutation.
clusterCellFrequencies
                        Clustering of cellular frequency probability
                        distributions
computeCellFrequencyDistributions
                        Gathering of cell frequency probability
                        distributions
plotSPs                 Subpopulation Visualization
roi                     Regions of interest
runExPANdS              Main Function
simulation              Simulated heterogeneous samples
snv                     Single Nucleotide Variations
