TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

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Documentation for package ‘TreeSummarizedExperiment’ version 1.0.3

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aggValue Perform data aggregations based on the available tree structures
colLinks TreeSummarizedExperiment-accessors
colLinks-method TreeSummarizedExperiment-accessors
colTree TreeSummarizedExperiment-accessors
colTree-method TreeSummarizedExperiment-accessors
countLeaf count the number of leaf nodes
countNode count the number of nodes
distNode Calculate the distance between any two nodes on the tree
findAncestor Find the ancestors of specified nodes
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
pruneTree remove branches of a phylo tree
rowLinks TreeSummarizedExperiment-accessors
rowLinks-method TreeSummarizedExperiment-accessors
rowTree TreeSummarizedExperiment-accessors
rowTree-method TreeSummarizedExperiment-accessors
shareNode Find the share node
signalNode find the optimal nodes to short result.
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
[-method TreeSummarizedExperiment-accessors