LinkDataFrame: A S4 class extended from DataFrame An S4 class LinkDataFrame
Construct a LinkDataFrame Construct a LinkDataFrame object
Perform data aggregations based on the available tree structures
Transfer between node number and node label
Calculate the distance between any two nodes on the tree
test all TSEs have DNAStringSet in the referenceSeq slot
test all TSEs have DNAStringSetList in the referenceSeq slot
rename a list automatically to avoid duplicated names
The links & trees in the specified dim are consistent
match a list of phylo (x.phys) against to a list of phylo (y.phys)
convert char. indicator to num. indicator
update dimLinks and dimTree (used in subsetByLeaf)
update the 'whichTree' column in row/column link data
To test whether the specified nodes are leaf nodes
phylo: A S3 class for the phylogenetic tree
Resolve loops 'resolveLoop' resolve loops by adding suffix to the child node. The suffix is "_i" where 'i' is a number. Please see examples.
A simulated phylogenetic tree with 10 tips and 9 internal nodes
Translate a data frame to a phylo object
list leaf nodes that are the descendants of at least one specified node