tree | R Documentation |
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)
).
data(tree)
A phylo object with 100 terminal nodes and 99 internal nodes.
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).
Caitlin Collins caitiecollins@gmail.com
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