CP.example              Example of cellularity and ploidy results
VarScan2seqz            Import VarScan output files, for use with the
                        Sequenza algorithm.
baf.bayes               Model allele-specific copy numbers with
                        specified cellularity and ploidy parameters
baf.model.fit           Model fitting using Bayesian inference
chromosome.view         A graphical representation of multiple
                        chromosomal features in parallel
cp.plot                 Plot log-posterior probability for the tested
                        values of cellularity and ploidy
example.seqz            Example "seqz" data
find.breaks             Segmentation of sequencing data using an
                        allele-specific copy number algorithm
gc.sample.stats         Normalize depth ratio values for GC-content
                        bias
get.ci                  Compute the confidence interval of cellularity
                        and ploidy
model.points            Generate mutation frequency and depth ratio
                        model point at given cellularity and ploidy
                        value
mutation.table          Identify mutations
plotWindows             Plot a windowed chromosome
read.seqz               Read an seqz or acgt format file
sequenza.extract        Sequenza convenience functions for standard
                        analysis
theoretical.baf         Calculates cellularity-dependent model points
types.matrix            Creates a dataframe of type tags
windowValues            Bins sequencing data for plotting
