Copy Number Estimation from Tumor Genome Sequencing Data

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Documentation for package ‘sequenza’ version 2.1.2

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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