RDocumentation
Moon
Learn R
Search all packages and functions
⚠️
There's a newer version (3.0.0) of this package.
Take me there.
sequenza (version 1.0.3)
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
Copy
Link to current version
Version
Version
3.0.0
2.1.2
2.1.1
2.1.0
2.0.0
1.0.5
1.0.4
1.0.3
1.0.2
1.0.1
Down Chevron
Install
install.packages('sequenza')
Monthly Downloads
111
Version
1.0.3
License
GPL-3
Homepage
http://cbs.dtu.dk/biotools/sequenza/
Maintainer
Francesco Favero
Last Published
December 12th, 2013
Functions in sequenza (1.0.3)
Search functions
model.points
Generate mutation frequency and depth ratio model point at given cellularity and ploidy value.
get.ci
Compute the confidence interval of cellularity and ploidy
plotWindows
Plot the specified windowed chromosome.
sequenza
Use sequenza to estimate tumor purity and ploidy.
gc.sample.stats
Normalize depth ratio values for GC-content bias
find.breaks
Segmentation of sequencing data using an allele-specific copy number algorithm
baf.bayes
Model allele-specific copy numbers with specified cellularity and DNA-content parameters
read.abfreq
Read an ABfreq or acgt format file
baf.model.fit
Model fitting using Bayesian inference
CP.example
Example of cellularity and ploidy results.
windowValues
Bins sequencing data for plotting
abf.data.abfreq
ABfreq file example.
types.matrix
Creates a dataframe of type tags
cp.plot
Plot log-likelihood for the tested values of cellularity and ploidy
chromosome.view
A graphical representation of multiple chromosomal features in parallel
theoretical.baf
Calculates cellularity-dependent model points
mutation.table
Extract mutations on homozygous position from an ABfreq file.