allAF |
Get allele frequencies for tumor data |

bootstrapEventTiming |
Bootstrap the results of eventTiming |

contAF |
Get allele frequencies for tumor data |

decontAF |
Get allele frequencies for tumor data |

divideGenome |
Helper functions for plotting |

errorAF |
Get allele frequencies for tumor data |

eventTiming |
Estimate the time of events in tumor data |

eventTimingOverList |
eventTiming for multiple samples and regions |

getPi0Summary |
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 |

numChromosome |
Helper functions for plotting |

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 coverage |

readSimulation |
Simulate reads based on an event matrix |