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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;
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Install
install.packages('sequenza')
Monthly Downloads
103
Version
1.0.4
License
GPL-3
Homepage
http://cbs.dtu.dk/biotools/sequenza/
Maintainer
Francesco Favero
Last Published
January 20th, 2014
Functions in sequenza (1.0.4)
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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.