Clonality testing


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Documentation for package ‘Clonality’ version 1.47.0

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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