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

sequenza (version 1.0.4)

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

1.0.4

License

GPL-3

Maintainer

Francesco Favero

Last Published

January 20th, 2014

Functions in sequenza (1.0.4)

plotWindows

Plot the specified windowed chromosome.
baf.bayes

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

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

Normalize depth ratio values for GC-content bias
types.matrix

Creates a dataframe of type tags
mutation.table

Extract mutations on homozygous position from an ABfreq file.
cp.plot

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

Read an ABfreq or acgt format file
baf.model.fit

Model fitting using Bayesian inference
sequenza

Use sequenza to estimate tumor purity and ploidy.
find.breaks

Segmentation of sequencing data using an allele-specific copy number algorithm
VarScan2abfreq

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

Bins sequencing data for plotting
chromosome.view

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

ABfreq file example.
theoretical.baf

Calculates cellularity-dependent model points
model.points

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

Example of cellularity and ploidy results.