# Clonality testing

## Documentation for package ‘Clonality’ version 1.42.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

Clonality-package | Clonality testing
ave.adj.probes | Averaging of adjacent probes in copy number arrays
chromosomePlots | Per-chromosome plots of the copy number arrays from a particular patient
Clonality | Clonality testing
clonality.analysis | Clonality testing using copy number data
clonEM | Auxiliary EM algorithm Function.
create.mutation.matrix | Formatting matrix of mutations
ECMtesting | Clonality testing of >=3 tumors using Extended Concordant Mutations (ECM) test based on LOH (Loss of Heterozygosity) profiles
freqdata | TCGA pancancer mutation frequencies
genomewidePlots | Plot of the genomewide copy number profiles of a pair of tumors.
get.mutation.frequencies | Estimating mutation frequencies based on the TCGA data or a submitted reference mutations file
grid.lik | Auxiliary function: Grid of conditional probabilities
histogramPlot | Histrograms of Log-Likelihood Ratios
lcis | Breast cancer data
LOHclonality | Clonality testing using LOH (Loss of Heterozygosity) profiles
LRtesting3or4tumors | Clonality testing of 3 or 4 tumors using Likelihood model based on LOH (Loss of Heterozygosity) profiles
model.lik | Auxiliary likelihood Function
mutation.proba | Probability of being clonal
mutation.rem | Estimation of the random-effect model for clonality based on mutations.
print.mutation.proba | Print for the mutation.proba function
print.mutation.rem | Print for the mutation.rem function
SNVtest | Testing relatedness (clonality) of two tumors from the same patient using profiles of somatic mutations
SNVtest2 | Test for tumors from 2 different sites
splitChromosomes | Chromosome splitting
xidens | Auxiliary function computing the density of xi