# Copy Number Estimation from Tumor Genome Sequencing Data

## Documentation for package ‘sequenza’ version 2.1.2

- 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 Bayesian inference
chromosome.view | A graphical representation of multiple chromosomal features in parallel
CP.example | Example of cellularity and ploidy results
cp.plot | Plot log-posterior probability for the tested values of cellularity and ploidy
cp.plot.contours | 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.norm | Normalize depth ratio values for GC-content bias
gc.sample.stats | Normalize depth ratio values for GC-content bias
genome.view | A graphical representation of multiple chromosomal features in parallel
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
mufreq.bayes | Model allele-specific copy numbers with specified cellularity and ploidy parameters
mufreq.model.fit | Model fitting using Bayesian inference
mutation.table | Identify mutations
plotWindows | Plot a windowed chromosome
read.acgt | Read an seqz or acgt format file
read.seqz | Read an 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-dependent model points
theoretical.depth.ratio | Calculates cellularity-dependent model points
theoretical.mufreq | Calculates cellularity-dependent model points
types.matrix | Creates a dataframe of type tags
VarScan2seqz | Import VarScan output files, for use with the Sequenza algorithm.
windowValues | Bins sequencing data for plotting