Man pages for IOstrovnaya/Clonality
Clonality testing
| ave.adj.probes | Averaging of adjacent probes in copy number arrays |
| chromosomePlots | Per-chromosome plots of the copy number arrays from a... |
| clonality.analysis | Clonality testing using copy number data |
| Clonality-internal | Internal Clonality functions |
| Clonality-package | Clonality testing |
| clonEM | Auxiliary EM algorithm Function. |
| create.mutation.matrix | Formatting matrix of mutations |
| ECMtesting | Clonality testing of >=3 tumors using Extended Concordant... |
| freqdata | TCGA pancancer mutation frequencies |
| genomewidePlots | Plot of the genomewide copy number profiles of a pair of... |
| get.mutation.frequencies | Estimating mutation frequencies based on the TCGA data or a... |
| 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... |
| model.lik | Auxiliary likelihood Function |
| mutation.proba | Probability of being clonal |
| mutation.rem | Estimation of the random-effect model for clonality based on... |
| 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... |
| SNVtest2 | Test for tumors from 2 different sites |
| splitChromosomes | Chromosome splitting |
| xidens | Auxiliary function computing the density of xi |
