Segmentation of single- and multi-track copy number data by penalized least squares regression.

aspcf | Allele-specific copy number segmentation. |

callAberrations | Call aberrations in segmented data |

getGRangesFormat | Get segments on the GRanges format |

imputeMissing | Impute missing copy number values |

interpolate.pcf | Interpolation of pcf-estimates. |

lymphoma | 3K aCGH data |

micma | Subset of 244K aCGH data |

multipcf | Multi-sample copy number segmentation. |

pcf | Single-sample copy number segmentation. |

pcfPlain | Plain single-sample copy number segmentation. |

plotAberration | Plot areas with copy number aberrations |

plotAllele | Plot SNP data and/or aspcf segmentation results |

plotChrom | Plot copy number data and/or segmentation results by... |

plotCircle | Plot a circular genome with aberration frequencies and... |

plotFreq | Plot percentage of samples with an aberration at a genomic... |

plotGamma | Plot segmentation results for several values of gamma |

plotGenome | Plot copy number data and/or segmentation results |

plotHeatmap | Plot copy number heatmap |

plotSample | Plot copy number data and/or segmentation results by sample |

selectSegments | Select multipcf segments |

SNPdata | Artificial SNP array data |

subsetData | Retrieve a data subset |

subsetSegments | Retrieve a subset of segments |

winsorize | Winsorization of copy number data |

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