SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing

admixtureRate | Estimate the admixture rate of normal cells in a tumor... |

collapse | Collapse measurements with a certain bin size. |

copynumberCorrected | Somatic copy number corrected by admixture rate. |

denoise | Smoothing procedure by replacing outliers. |

GCbiasRemoval | Correct GC bias for read depth ratio of each site. |

GCcontent | GC content for hg19 human genome at each 1Mb interval. |

GCcount | Calculate the GC content of given window size for a... |

larsCBSsegment | Segmentation based on Circular Binary Segmentation followed... |

MergeSegment | Merge neighboring segments with same somatic copy number and... |

plotSegment | Plot segmentation. |

plotSubclonality | Plot clonality and somatic copy number. |

refineSegment | Refine the segmentation based on estimated somatic ratio. |

segmentGCbiasRemoval | Correct GC bias for read depth ratio of each segment. |

segwithratio | Segments with somatic ratio. |

SomatiCAFormat-methods | ~~ Methods for Function 'SomatiCAFormat' in Package... |

SomatiCA-package | Identifying, characterizing and quantifying somatic copy... |

SomatiCApipe | SomatiCA pipeline. |

SomatiCAUsersGuide | View SomatiCA User's Guide |

somaticRatio | Estimate somatic ratio for given segments. |

subclonality | Estimate subclonality for each somatic copy number... |

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