tests/testthat/test-imputeIntensity.R

In HimesGroup/qmtools: Quantitative Metabolomics Data Processing Tools

test_that("imputeIntensity works for SummarizedExperiment.", {

    for (method in setdiff(imputation_methods, c("mixed", "with", "MLE", 
                                                 "none", "nbavg"))) {
        set.seed(1e7)
        se <- imputeIntensity(faahko_sub, i = 1, name = "imp", method = method)
        expect_s4_class(se, "SummarizedExperiment")
        expect_false(anyNA(assay(se, "imp")))

        ## No name argument returns a matrix
        set.seed(1e7)
        out1 <- imputeIntensity(faahko_sub, i = 1, method = method)
        expect_true(is.matrix(out1))
        expect_false(anyNA(out1))

        ## Matrix input returns a matrix
        m <- assay(faahko_sub, 1)
        set.seed(1e7)
        out2 <- imputeIntensity(m, method = method)
        expect_true(is.matrix(out2))
        expect_false(anyNA(out2))

        expect_equal(assay(se, "imp"), out1)
        expect_equal(out1, out2)
    }

    ## mixed
    randna <- apply(assay(faahko_sub, 1), 1, anyNA)
    expect_error(
        imputeIntensity(faahko_sub, i = 1, method = "mixed",
                        randna = randna, mnar = "min"),
        regexp = "mar"
    )
    expect_error(
        imputeIntensity(faahko_sub, i = 1, method = "mixed",
                        randna = randna, mar = "knn"),
        regexp = "mnar"
    )
    expect_error(
        imputeIntensity(faahko_sub, i = 1, method = "mixed",
                        mnar = "min", mar = "knn"),
        regexp = "randna"
    )
    expect_error(
        imputeIntensity(faahko_sub, i = 1, method = "mixed", randna = TRUE,
                        mnar = "min", mar = "knn"),
        regexp = "randna"
    )
    out <- imputeIntensity(faahko_sub, i = 1, method = "mixed", randna = randna,
                           mnar = "min", mar = "knn")
    expect_false(anyNA(out))

    ## none
    out <- imputeIntensity(faahko_sub, i = 1, method = "none")
    expect_identical(out, assay(faahko_sub, 1))
})

test_that("imputeKNN works.", {
    m <- assay(faahko_sub, 1)

    ## Gower
    out_g <- imputeKNN(m, by = "sample", type = "gower")
    expect_false(anyNA(out_g))

    ## Euclidean
    out_e <- imputeKNN(m, type = "euclidean", scale = TRUE)
    expect_false(anyNA(out_e))
    expect_error(
        imputeKNN(m, type = "zzz")
    )
})