Expanding Ploidy and Allele-Frequency on Nested Subpopulations

assignMutations | Mutation Assignment |

assignQuantityToMutation | Quantity assignment (copy number) to mutations |

assignQuantityToSP | Quantity assignment (copy number) to subpopulations |

buildMultiSamplePhylo | Relations between inter- and intra-sample subpopulations |

buildPhylo | Relations between subpopulations |

cbs | Matrix of copy number fragments |

cellfrequency_pdf | Computes the probability distribution of cellular frequencies... |

clusterCellFrequencies | Clustering of cellular frequency probability distributions |

computeCellFrequencyDistributions | Gathering of cell frequency probability distributions |

gatherEXPANDSoutput | Reading EXPANDS' output files |

plotSPs | Subpopulation Visualization |

roi | Regions of interest |

runExPANdS | Main Function |

simulation | Simulated heterogeneous samples |

snv | Single Nucleotide Variations |

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