Copy Number Estimation from Tumor Genome Sequencing Data


[Up] [Top]

Documentation for package ‘sequenza’ version 3.0.0

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