CP.example              Example of cellularity and ploidy results
baf.bayes               Model allele-specific copy numbers with
                        specified cellularity and ploidy parameters
baf.model.fit           Model fitting using maximum a posteriori
                        inference
chromosome.view         A graphical representation of multiple
                        chromosomal features
cp.plot                 Plot log-posterior probability for the output
                        of the 'sequenza.fit' function
example.seqz            Example "seqz" data
find.breaks             Segmentation of sequencing data using an
                        allele-specific copy number algorithm
gc.sample.stats         Collect display and correct GC-content related
                        coverage bias
model.points            Generate B-allele frequency, mutation frequency
                        and depth ratios at given model points,
                        cellularity and ploidy values
mutation.table          Identify mutations
plotWindows             Plot a binned values of a chromosome
read.seqz               Read a seqz or acgt format file
sequenza.extract        Sequenza convenience functions for standard
                        analysis
theoretical.baf         Calculates cellularity and ploidy dependent
                        model points
types.matrix            Creates a matrix of type tags
windowValues            Bins sequencing data for plotting
