Estimation of Temporal Ordering of Cancer Abnormalities

alleleFreq | Get allele frequencies for tumor data |

bootstrapEventTiming | Bootstrap the results of eventTiming |

eventTiming | Estimate the time of events in tumor data |

eventTimingOverList | eventTiming for multiple samples and regions |

hg19chromosomes | Definitions of the p,q, and centromeres of chromosomes |

labelSeg | Helper functions for plotting |

makeEventHistory | Create the event history matrix |

mleAF | Estimate the most likely allele frequency |

multidensity | plot multiple density functions on top of each other |

mut2Seg | Align mutations to segments |

mutData | Example Mutation Data |

plotAlleleByPosition | Plot allele frequencies by position |

plotAlleleDensity | Plot density/histogram of allele frequencies |

plotCopies | plot segmentation values against each other |

plotPi0 | Confidence intervals for pi[0] |

plotSegmentation | plot segmentation(s) against positions |

plotSeqCount | Basic function for plotting the ratio of tumor to normal... |

readSimulation | Simulate reads based on an event matrix |

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