# TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

## Documentation for package ‘TreeSummarizedExperiment’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

TreeeSummarizedExperiment-package | The 'TreeSummarizedExperiment' package
addLabel | add labels to nodes of a tree
aggTSE | Perform data aggregations based on the available tree structures
aggValue | Perform data aggregations based on the available tree structures
asLeaf | change internal nodes to leaf nodes
cbind-method | Combine TSEs by rows or columns
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
colTree<- | TreeSummarizedExperiment-accessors
colTree<--method | TreeSummarizedExperiment-accessors
colTreeNames | TreeSummarizedExperiment-accessors
colTreeNames-method | TreeSummarizedExperiment-accessors
colTreeNames<- | TreeSummarizedExperiment-accessors
colTreeNames<--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
joinNode | Join 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
makeTSE | A toy TreeSummarizedExperiment object
matTree | Transform a phylo object into a matrix.
printNode | To print out the node labels
rbind-method | Combine TSEs by rows or columns
referenceSeq | TreeSummarizedExperiment-accessors
referenceSeq-method | TreeSummarizedExperiment-accessors
referenceSeq<- | TreeSummarizedExperiment-accessors
referenceSeq<--method | TreeSummarizedExperiment-accessors
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
rowTree<- | TreeSummarizedExperiment-accessors
rowTree<--method | TreeSummarizedExperiment-accessors
rowTreeNames | TreeSummarizedExperiment-accessors
rowTreeNames-method | TreeSummarizedExperiment-accessors
rowTreeNames<- | TreeSummarizedExperiment-accessors
rowTreeNames<--method | TreeSummarizedExperiment-accessors
shareNode | Find the share node
showNode | Find nodes on the tree
signalNode | Join nodes
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-combine | Combine TSEs by rows or columns
TreeSummarizedExperiment-constructor | Construct a TreeSummarizedExperiment object
unionLeaf | list leaf nodes that are the descendants of at least one specified node
updateObject-method | Update a 'TreeSummarizedExperiment' object
[-method | TreeSummarizedExperiment-accessors
[<--method | TreeSummarizedExperiment-accessors