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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 |
| ECMtesting | Clonality testing of >=3 tumors using Extended Concordant Mutations (ECM) test based on LOH (Loss of Heterozygosity) profiles |
| genomewidePlots | Plot of the genomewide copy number profiles of a pair of tumors. |
| histogramPlot | Histrograms of Log-Likelihood Ratios |
| 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 |
| splitChromosomes | Chromosome splitting |