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sequenza (version 1.0.3)

Analysis and visualization of tumor sequencing data.

Description

This package provides tools to analyze NGS data, including cellularity and ploidy estimation; mutation and copy number detection and quantification;

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Version

Install

install.packages('sequenza')

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Version

1.0.3

License

GPL-3

Homepage

http://cbs.dtu.dk/biotools/sequenza/

Maintainer

Francesco Favero

Last Published

December 12th, 2013

Functions in sequenza (1.0.3)

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

plotWindows

Plot the specified windowed chromosome.

sequenza

Use sequenza to estimate tumor purity and ploidy.

gc.sample.stats

Normalize depth ratio values for GC-content bias

find.breaks

Segmentation of sequencing data using an allele-specific copy number algorithm

baf.bayes

Model allele-specific copy numbers with specified cellularity and DNA-content parameters

read.abfreq

Read an ABfreq or acgt format file

baf.model.fit

Model fitting using Bayesian inference

CP.example

Example of cellularity and ploidy results.

windowValues

Bins sequencing data for plotting

abf.data.abfreq

ABfreq file example.

types.matrix

Creates a dataframe of type tags

cp.plot

Plot log-likelihood for the tested values of cellularity and ploidy

chromosome.view

A graphical representation of multiple chromosomal features in parallel

theoretical.baf

Calculates cellularity-dependent model points

mutation.table

Extract mutations on homozygous position from an ABfreq file.