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sequenza (version 1.0.1)

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')

Monthly Downloads

4

Version

1.0.1

License

GPL-3

Maintainer

Francesco Favero

Last Published

December 2nd, 2013

Functions in sequenza (1.0.1)

read.abfreq

Read an ABfreq or acgt format file
types.matrix

Creates a dataframe of type tags
windowValues

Bins sequencing data for plotting
model.points

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

Plot the specified windowed chromosome.
theoretical.baf

Calculates cellularity-dependent model points
sequenza

Use sequenza to estimate tumor purity and ploidy.
abf.data.abfreq

ABfreq file example.
CP.example

Example of cellularity and ploidy results.
baf.bayes

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

Extract mutations on homozygous position from an ABfreq file.
get.ci

Compute the confidence interval of cellularity and ploidy
baf.model.fit

Model fitting using Bayesian inference
gc.sample.stats

Normalize depth ratio values for GC-content bias
find.breaks

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

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

A graphical representation of multiple chromosomal features in parallel