# Copy Number Estimation from Tumor Genome Sequencing Data

## Documentation for package ‘sequenza’ version 3.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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