tests/testthat/test-splatPopEstimate.R

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

context("splatPopEstimate")
seed <- 49
if (requireNamespace("VariantAnnotation", quietly = TRUE) &&
    requireNamespace("preprocessCore", quietly = TRUE)) {
    # Mock data
    bulk.means <- mockBulkMatrix(n.genes = 50, n.samples = 10, seed = seed)
    bulk.eqtl <- mockBulkeQTL(n.genes = 50, seed = seed)
    set.seed(seed)
    counts <- scuttle::mockSCE()
}

test_that("splatPopEstimate works", {
    skip_if_not_installed("VariantAnnotation")
    skip_if_not_installed("preprocessCore")
    # Check separate functions
    params <- splatPopEstimateMeanCV(newSplatPopParams(), bulk.means)
    expect_true(validObject(params))
    params <- splatPopEstimateEffectSize(newSplatPopParams(), bulk.eqtl)
    expect_true(validObject(params))

    # Check full function
    params <- splatPopEstimate(
        means = bulk.means,
        eqtl = bulk.eqtl,
        counts = counts
    )
    expect_true(validObject(params))
})

test_that("splatPopEstimate checks on input data", {
    skip_if_not_installed("VariantAnnotation")
    skip_if_not_installed("preprocessCore")
    bulk.eqtl.bad <- bulk.eqtl
    bulk.eqtl.bad$gene_id <- NULL
    expect_error(
        splatPopEstimate(
            means = bulk.means,
            eqtl = bulk.eqtl.bad,
            counts = counts
        ),
        "Incorrect format for eqtl data."
    )

    bulk.means.bad <- bulk.means
    bulk.means.bad[, 1] <- NA
    expect_error(
        splatPopEstimate(
            means = bulk.means.bad,
            eqtl = bulk.eqtl,
            counts = counts
        ),
        "Incorrect format or NAs present in emp.gene.means."
    )
})