tests/testthat/test_association.R

In Gibbons-Lab/mbtools: Provides helper functions for microbiome preprocessing and analysis

context("association tests")

flog.threshold(WARN)

otus <- sapply(seq(2, 4, length.out = 20),
    function(i) rpois(6, 10 ^ i))
otus <- otus * (1:6)
rownames(otus) <- paste("sample", 1:6)
colnames(otus) <- paste("taxa", 1:20)
tax <- matrix(rep(LETTERS[1:20]), ncol = 1)
colnames(tax) <- "genus"
rownames(tax) <- colnames(otus)
sdata <- data.frame(val = 1:6, sex = factor(rep(c("M", "F"), 3)))
rownames(sdata) <- rownames(otus)
ps <- phyloseq(otu_table(otus, taxa_are_rows = FALSE), tax_table(tax),
               sample_data(sdata))

test_that("DESeq2 works", {
    tests <- association(ps, independent_weighting = FALSE)
    expect_equal(nrow(tests), 40)

    tests <- association(ps, confounders = "sex",
                         independent_weighting = FALSE)
    expect_equal(nrow(tests), 20)
})

test_that("limma works", {
    tests <- association(ps, method = "voom", independent_weighting = FALSE)
    expect_equal(nrow(tests), 40)

    tests <- association(ps, method = "voom",
                         confounders = "sex",
                         independent_weighting = FALSE)
    expect_equal(nrow(tests), 20)
})

test_that("CLR works", {
    tests <- association(ps, method = "clr", independent_weighting = FALSE)
    expect_equal(nrow(tests), 40)

    tests <- association(ps, method = "clr",
                         confounders = "sex",
                         independent_weighting = FALSE)
    expect_equal(nrow(tests), 20)
})

# -- deprecated --
# test_that("combinatorial works", {
#     sample_data(ps)$cat <- factor(rep(LETTERS[1:3], 2))
#     tests <- combinatorial_association(ps,
#         variable = "cat", independent_weighting = FALSE)
#     expect_equal(nrow(tests), 60)
# })

flog.threshold(INFO)