baf.bayes |
Model allele-specific copy numbers with specified cellularity and ploidy parameters |
baf.model.fit |
Model fitting using Bayesian inference |
chromosome.view |
A graphical representation of multiple chromosomal features in parallel |
CP.example |
Example of cellularity and ploidy results |
cp.plot |
Plot log-posterior probability for the tested values of cellularity and ploidy |
cp.plot.contours |
Plot log-posterior probability for the tested values of cellularity and ploidy |
example.seqz |
Example "seqz" data |
find.breaks |
Segmentation of sequencing data using an allele-specific copy number algorithm |
gc.norm |
Normalize depth ratio values for GC-content bias |
gc.sample.stats |
Normalize depth ratio values for GC-content bias |
genome.view |
A graphical representation of multiple chromosomal features in parallel |
get.ci |
Compute the confidence interval of cellularity and ploidy |
model.points |
Generate mutation frequency and depth ratio model point at given cellularity and ploidy value |
mufreq.bayes |
Model allele-specific copy numbers with specified cellularity and ploidy parameters |
mufreq.model.fit |
Model fitting using Bayesian inference |
mutation.table |
Identify mutations |
plotWindows |
Plot a windowed chromosome |
read.acgt |
Read an seqz or acgt format file |
read.seqz |
Read an 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-dependent model points |
theoretical.depth.ratio |
Calculates cellularity-dependent model points |
theoretical.mufreq |
Calculates cellularity-dependent model points |
types.matrix |
Creates a dataframe of type tags |
VarScan2seqz |
Import VarScan output files, for use with the Sequenza algorithm. |
windowValues |
Bins sequencing data for plotting |