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