tests/testthat/test_results.R

In lpantano/DEGreport: Report of DEG analysis

context("results")
library(DESeq2)

dds <- makeExampleDESeqDataSet(betaSD=1)
colData(dds)[["treatment"]] <- sample(colData(dds)[["condition"]], 12)
design(dds) <-  ~ condition + treatment
dds <- DESeq(dds)
res <- results(dds)
resComps <- degComps(dds, contrast = c("condition_B_vs_A"))

test_that("Combinations", {
    # expect_named(.guessComb(dds,
    #                         combs = c("condition"),
    #                         contrast = list("treatment_B_vs_A", c("condition", "A", "B")),
    #                         pairs = TRUE),
    #              c("condition_1_vs_2",
    #                "treatment_B_vs_A",
    #                "condition_A_vs_B"))
    expect_type(.normalizeNames(c("condition", 2), dds), "character")
    expect_output(.createComb(dds, c("treatment", "condition")) %>% str,
                  "List of 2")
})

test_that("Results",{
    # expect_match(.guessResults(dds, c("condition", "A", "B"), 0.05) %>% class,
    #             "DESeqResults")
    # expect_match(.guessResults(dds, "condition_B_vs_A", 0.05) %>% class,
    #             "DESeqResults")
    expect_error(.guessResults(dds, "condition_C_vs_A", 0.05))
    # expect_match(.guessShrunken(dds, c("condition", "A", "B"), res, "normal") %>%
    #                  class,
    #              "DESeqResults")
    expect_error(.guessResults(dds, "condition_C_vs_A", res))
    expect_type(degSummary(dds, contrast = "condition_B_vs_A"), "list")
    expect_type(degSummary(res), "list")
    expect_type(degSummary(resComps), "list")
    expect_error(degSummary(colData(dds)))
    expect_output(degSummary(res, kable = TRUE), "|")
})

test_that("Correct", {
    res <- .guessResults(dds, c("condition", "A", "B"), 0.05, "default")
    #expect_s4_class(.correct_fdr(res, "lfdr-stat"), "DESeqResults")
    #expect_s4_class(.correct_fdr(res, "lfdr-pvalue"), "DESeqResults")
    expect_error(.correct_fdr(res, "other"))
    expect_equal(res, .correct_fdr(res, "default"))
})