Clonality testing

---

Documentation for package ‘Clonality’ version 1.46.0

• 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