Learn R Programming
⚠️There's a newer version (3.0.0) of this package.Take me there.

sequenza (version 1.0.2)

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;

Copy Link

Version

Install

install.packages('sequenza')

Monthly Downloads

4

Version

1.0.2

License

GPL-3

Maintainer

Francesco Favero

Last Published

December 4th, 2013

Functions in sequenza (1.0.2)

find.breaks

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

ABfreq file example.
get.ci

Compute the confidence interval of cellularity and ploidy
gc.sample.stats

Normalize depth ratio values for GC-content bias
windowValues

Bins sequencing data for plotting
mutation.table

Extract mutations on homozygous position from an ABfreq file.
chromosome.view

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

Creates a dataframe of type tags
plotWindows

Plot the specified windowed chromosome.
baf.bayes

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

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

Read an ABfreq or acgt format file
sequenza

Use sequenza to estimate tumor purity and ploidy.
theoretical.baf

Calculates cellularity-dependent model points
baf.model.fit

Model fitting using Bayesian inference
CP.example

Example of cellularity and ploidy results.
model.points

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