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| addLabel | add labels to nodes of a tree |
| aggValue | Perform data aggregations based on the available tree structures |
| asLeaf | change internal nodes to leaf nodes |
| changeTree | Change the row or column tree |
| colLinks | TreeSummarizedExperiment-accessors |
| colLinks-method | TreeSummarizedExperiment-accessors |
| colnames<--method | TreeSummarizedExperiment-accessors |
| colTree | TreeSummarizedExperiment-accessors |
| colTree-method | TreeSummarizedExperiment-accessors |
| 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 |
| findAncestor | Find the ancestors of specified nodes |
| findChild | Find the children |
| findDescendant | Find descendants (or offsprings) |
| findOS | Find descendants (or offsprings) |
| findSibling | find the sibling node |
| isLeaf | To test whether the specified nodes are leaf nodes |
| LinkDataFrame | Construct a LinkDataFrame Construct a LinkDataFrame object |
| LinkDataFrame-class | LinkDataFrame: A S4 class extended from DataFrame An S4 class LinkDataFrame |
| LinkDataFrame-constructor | Construct a LinkDataFrame Construct a LinkDataFrame object |
| matTree | Transform a phylo object into a matrix. |
| printNode | To print out the node labels |
| resolveLoop | Resolve loops 'resolveLoop' resolve loops by adding suffix to the child node. The suffix is "_i" where 'i' is a number. Please see examples. |
| rowLinks | TreeSummarizedExperiment-accessors |
| rowLinks-method | TreeSummarizedExperiment-accessors |
| rownames<--method | TreeSummarizedExperiment-accessors |
| rowTree | TreeSummarizedExperiment-accessors |
| rowTree-method | TreeSummarizedExperiment-accessors |
| shareNode | Find the share node |
| showNode | Find nodes on the tree |
| signalNode | find the optimal nodes to short result. |
| subsetByNode | TreeSummarizedExperiment-accessors |
| subsetByNode-method | TreeSummarizedExperiment-accessors |
| tinyTree | A simulated phylogenetic tree with 10 tips and 9 internal nodes |
| toTree | Translate a data frame to a phylo object |
| trackNode | track the nodes of a phylo tree |
| transNode | Transfer between node number and node label |
| TreeSummarizedExperiment | Construct a TreeSummarizedExperiment object |
| 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 specified node |
| [-method | TreeSummarizedExperiment-accessors |