TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

addLabel | add labels to nodes of a tree |

aggValue | Perform data aggregations based on the available tree... |

asLeaf | change internal nodes to leaf nodes |

changeTree | Change the row or column tree |

convertNode | Transfer between node number and node label |

countLeaf | count the number of leaf nodes |

countNode | count the number of nodes |

detectLoop | Detect loops 'detectLoop' detects loops |

distNode | Calculate the distance between any two nodes on the tree |

dot-checkLDF | 'validLDF' is to valid a 'LinkDataFrame' object. |

dot-checkTSE | valid TreeSummarizedExperiment class |

findAncestor | Find the ancestors of specified nodes |

findChild | Find the children |

findDescendant | Find descendants (or offsprings) |

findSibling | find the sibling node |

isLeaf | To test whether the specified nodes are leaf nodes |

LinkDataFrame-class | LinkDataFrame: A S4 class extended from DataFrame An S4 class... |

LinkDataFrame-constructor | Construct a LinkDataFrame Construct a LinkDataFrame object |

matTree | Transform a phylo object into a matrix. |

phylo | phylo: A S3 class for the phylogenetic tree |

printNode | To print out the node labels |

resolveLoop | Resolve loops 'resolveLoop' resolve loops by adding suffix to... |

shareNode | Find the share node |

showNode | Find nodes on the tree |

signalNode | find the optimal nodes to short result. |

tinyTree | A simulated phylogenetic tree with 10 tips and 9 internal... |

toTree | Translate a data frame to a phylo object |

trackNode | track the nodes of a phylo tree |

TreeSummarizedExperiment-accessor | TreeSummarizedExperiment-accessors |

TreeSummarizedExperiment-class | An S4 class TreeSummarizedExperiment |

TreeSummarizedExperiment-constructor | Construct a TreeSummarizedExperiment object |

unionLeaf | list leaf nodes that are the descendants of at least one... |

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