pair.tests: Pairwise tests for categorical phenotypes

In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

Pairwise tests for categorical phenotypes

Description

Internal function to calculate treeWAS terminal, simultaneous, subsequent tests, and chi-squared p-values for a given snp across pairs of phenotype levels.

Usage

pair.tests(x, y, z, method = "bonf", digits = 3)

Arguments

x	A contingency table (snps[,i] x phen) for score 1 (terminal.test with correct.prop = TRUE, categorical = TRUE).
y	A vector of values containing pairwise score 2 (simultaneous.test with categorical = TRUE) results for snps[,i].
z	A contingency table (snps.rec[,i] x phen.rec) for score 3 (subsequent.test with correct.prop = TRUE, categorical = TRUE).

Author(s)

Caitlin Collins [e-mail]

Examples

## Example ##
## Not run: 
## basic use of fn
out <- pair.tests(x, y, z)

## End(Not run)

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