panther-tree: Reads PANTHER db trees

In USCbiostats/phylogenetic: Statistical Inference and Prediction of Annotations in Phylogenetic Trees

Reads PANTHER db trees

Description

The PANTHER Project handles a modified version of newick tree files which, besides of the tree structure, includes the type of node and ancestor labels. This function is a wrapper of ape::read.tree().

Usage

read_panther(x, tree.reader = ape::read.tree, ...)

read.panther(x, tree.reader = ape::read.tree, ...)

Arguments

x	Character scalar. Full path to the panther file.
tree.reader	Function that will be used to read the tree file. It can be either ape::read.tree or rncl::read_newick_phylo.
...	Further arguments passed to ape::read.tree().

Value

A list consisting of a data.frame and a phylo object. The data.frame has the following columns:

branch_length	Numeric vector. Length of the branch to its parent node.
type	Character vector. Can be either "S" (speciation), "D" (duplication), or "T" (horizontal transfer).
ancestor	Character vector. Name of the ancestor.

The nodeids can be identified using the rownames.

See Also

Other reading: read_nhx(), read_pli()

Examples

path <- system.file("tree.tree", package="aphylo")
read_panther(path)

USCbiostats/phylogenetic documentation built on Oct. 28, 2023, 7:23 a.m.