Base Classes for Storing Genomic Interaction Data

boundingBox | Get the bounding box |

ContactMatrix-accessors | ContactMatrix accessors |

ContactMatrix-class | ContactMatrix class and constructors |

ContactMatrix-distances | Compute linear distances from ContactMatrix objects |

ContactMatrix-overlaps | Find overlaps between GRanges and a ContactMatrix |

ContactMatrix-sorting | ContactMatrix sorting and ordering |

ContactMatrix-subset | ContactMatrix subsetting and combining |

conversion | Convert between classes |

distances | Get the linear distance for each interaction |

GInteractions-class | GInteractions class and constructors |

granges-methods | Equivalents of GRanges methods |

interaction-accessors | Interaction accessors |

interaction-bind | Interaction combining |

interaction-compare | Interaction comparisons |

InteractionSet-class | InteractionSet class and constructors |

interaction-subset | Interaction subsetting and combining |

linearize | Linearize 2D interactions into 1D ranges |

linkOverlaps | Link overlapping regions |

overlaps | Find overlaps between interactions in one or two dimensions |

pairs | Extract paired ranges |

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