baf.bayes |
Model allele-specific copy numbers with specified cellularity and ploidy parameters |
baf.model.fit |
Model fitting using maximum a posteriori inference |
baf.model.points |
Generate B-allele frequency, mutation frequency and depth ratios at given model points, cellularity and ploidy values |
baf.types.matrix |
Creates a matrix of type tags |
chromosome.view |
A graphical representation of multiple chromosomal features |
CP.example |
Example of cellularity and ploidy results |
cp.plot |
Plot log-posterior probability for the output of the 'sequenza.fit' function |
cp.plot.contours |
Plot log-posterior probability for the output of the 'sequenza.fit' function |
example.seqz |
Example "seqz" data |
find.breaks |
Segmentation of sequencing data using an allele-specific copy number algorithm |
gc.sample.stats |
Collect display and correct GC-content related coverage bias |
gc.summary.plot |
Collect display and correct GC-content related coverage bias |
genome.view |
A graphical representation of multiple chromosomal features |
get.ci |
Plot log-posterior probability for the output of the 'sequenza.fit' function |
mean_gc |
Collect display and correct GC-content related coverage bias |
median_gc |
Collect display and correct GC-content related coverage bias |
model.points |
Generate B-allele frequency, mutation frequency and depth ratios at given model points, cellularity and ploidy values |
mufreq.bayes |
Model allele-specific copy numbers with specified cellularity and ploidy parameters |
mufreq.model.fit |
Model fitting using maximum a posteriori inference |
mufreq.model.points |
Generate B-allele frequency, mutation frequency and depth ratios at given model points, cellularity and ploidy values |
mufreq.types.matrix |
Creates a matrix of type tags |
mutation.table |
Identify mutations |
plotWindows |
Plot a binned values of a chromosome |
read.acgt |
Read a seqz or acgt format file |
read.seqz |
Read a seqz or acgt format file |
segment.breaks |
Segmentation of sequencing data using an allele-specific copy number algorithm |
sequenza.extract |
Sequenza convenience functions for standard analysis |
sequenza.fit |
Sequenza convenience functions for standard analysis |
sequenza.results |
Sequenza convenience functions for standard analysis |
theoretical.baf |
Calculates cellularity and ploidy dependent model points |
theoretical.depth.ratio |
Calculates cellularity and ploidy dependent model points |
theoretical.mufreq |
Calculates cellularity and ploidy dependent model points |
types.matrix |
Creates a matrix of type tags |
windowBf |
Bins sequencing data for plotting |
windowValues |
Bins sequencing data for plotting |