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sequenza (version 2.1.0)

Copy number estimation from tumor genome sequencing data.

Description

This package provides 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

4

Version

2.1.0

License

GPL-3

Maintainer

Francesco Favero

Last Published

October 8th, 2014

Functions in sequenza (2.1.0)

theoretical.baf

Calculates cellularity-dependent model points
plotWindows

Plot a windowed chromosome
find.breaks

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

Model fitting using Bayesian inference
model.points

Generate mutation frequency and depth ratio model point at given cellularity and ploidy value
get.ci

Compute the confidence interval of cellularity and ploidy
mutation.table

Identify mutations
chromosome.view

A graphical representation of multiple chromosomal features in parallel
types.matrix

Creates a dataframe of type tags
cp.plot

Plot log-posterior probability for the tested values of cellularity and ploidy
windowValues

Bins sequencing data for plotting
sequenza

Sequenza convenience functions for standard analysis
read.seqz

Read an seqz or acgt format file
example.seqz

Example seqz data
CP.example

Example of cellularity and ploidy results
VarScan2seqz

Import VarScan output files, for use with the Sequenza algorithm.
gc.sample.stats

Normalize depth ratio values for GC-content bias
baf.bayes

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