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sequenza (version 1.0.5)

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

38

Version

1.0.5

License

GPL-3

Maintainer

Francesco Favero

Last Published

February 11th, 2014

Functions in sequenza (1.0.5)

CP.example

Example of cellularity and ploidy results.
theoretical.baf

Calculates cellularity-dependent model points
plotWindows

Plot the specified windowed chromosome.
chromosome.view

A graphical representation of multiple chromosomal features in parallel
abf.data.abfreq

ABfreq file example.
read.abfreq

Read an ABfreq or acgt format file
mutation.table

Extract mutations on homozygous position from an ABfreq file.
types.matrix

Creates a dataframe of type tags
cp.plot

Plot log-likelihood for the tested values of cellularity and ploidy
VarScan2abfreq

Import varscan output files, to be able to use it with sequenza algorithm.
sequenza

Use sequenza to estimate tumor purity and ploidy.
model.points

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

Bins sequencing data for plotting
gc.sample.stats

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

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

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

Model fitting using Bayesian inference
baf.bayes

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