simultaneous.test: Simultaneous test
In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

simultaneous.test

R Documentation

Simultaneous test

Description

Calculates treeWAS score 2, the simultaneous test, as the number of substitutions or changes in genotype (snps.reconstruction) and phenotype (phen.reconstruction) that occur simultaneously on the same branches of the tree.

Usage

simultaneous.test(
  snps.reconstruction,
  phen.reconstruction,
  tree,
  categorical = FALSE
)

Arguments

`snps.reconstruction`	A matrix containing the terminal and reconstructed ancestral states of SNPs for all nodes in the tree.
`phen.reconstruction`	A vector containing the terminal and reconstructed ancestral states of the phenotype for all nodes in the tree.
`tree`	A phylo object containing the tree representing the ancestral relationships between the individuals for which snps and phen are known.