tree: A phylogenetic tree.
In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

tree	R Documentation

A phylogenetic tree.

Description

This phylogenetic tree is a phylo object (see vignette("Trees", package="phangorn")) connecting the individuals represented in the rows of the example genetic data matrix (see: data(snps)) and the elements of the example phenotypic vector (see: data(phen)).

Usage

data(tree)

Format

A phylo object with 100 terminal nodes and 99 internal nodes.

Details

In this case, the tree was generated via simulation and used to simulate the genotypic and phenotypic data. In a typical empirical analysis, however, a phylogenetic tree would represent the inferred ancestral relationships between individuals, and it would be estimated from the available genetic data. For example, such a phylogeny could be reconstructed using tree.reconstruct(snps, method="NJ"), or automatically generated within treeWAS, according to the tree argument, as in: treeWAS(snps, phen, tree="NJ") (see the treeWAS vignette).