get.ancestral.pars: Ancestral sequence reconstruction via parsimony

In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

Ancestral sequence reconstruction via parsimony

Description

A wrapper for the ancestral.pars function from ape. Can perform parsimonious ASR for variables in matrix or vector form.

Usage

get.ancestral.pars(var, tree, unique.cols = FALSE)

Arguments

var	A matrix or vector containing a variable whose state at ancestral nodes we want to infer.
tree	A phylo object containing a phylogenetic tree whose tips contain the same individuals as are in the elements of var, if var is a vector, or in the rows of var, if var is a matrix.

Details

Note that the (row)names of var should match the tip.labels of tree.

Author(s)

Caitlin Collins [e-mail]

caitiecollins/treeWAS documentation built on March 9, 2024, 3:15 p.m.