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sequenza (version 3.0.0)

Copy Number Estimation from Tumor Genome Sequencing Data

Description

Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.

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Version

Install

install.packages('sequenza')

Monthly Downloads

38

Version

3.0.0

License

GPL-3

Maintainer

Francesco Favero

Last Published

May 9th, 2019

Functions in sequenza (3.0.0)

chromosome.view

A graphical representation of multiple chromosomal features
model.points

Generate B-allele frequency, mutation frequency and depth ratios at given model points, cellularity and ploidy values
cp.plot

Plot log-posterior probability for the output of the sequenza.fit function
mutation.table

Identify mutations
baf.bayes

Model allele-specific copy numbers with specified cellularity and ploidy parameters
windowValues

Bins sequencing data for plotting
sequenza

Sequenza convenience functions for standard analysis
find.breaks

Segmentation of sequencing data using an allele-specific copy number algorithm
baf.model.fit

Model fitting using maximum a posteriori inference
CP.example

Example of cellularity and ploidy results
theoretical.baf

Calculates cellularity and ploidy dependent model points
types.matrix

Creates a matrix of type tags
example.seqz

Example “seqz” data
gc.sample.stats

Collect display and correct GC-content related coverage bias
plotWindows

Plot a binned values of a chromosome
read.seqz

Read a seqz or acgt format file