tests/testthat/test-k_qsvs.R

In LieberInstitute/qsvaR: Generate Quality Surrogate Variable Analysis for Degradation Correction

mod <- model.matrix(~ mitoRate + Region + rRNA_rate + totalAssignedGene + RIN, data = colData(rse_tx))

# rse_tx_low has low expression
rse_tx_low <- rse_tx[rowMeans(assays(rse_tx)$tpm) < 1, ]

# mod2 is not full rank
mod2 <- mod
mod2 <- cbind(mod2, 1 - mod[, "mitoRate"])
colnames(mod2)[8] <- "mitotest"

## Set a random seed
set.seed(20230621)
k_res <- k_qsvs(rse_tx, mod, "tpm")

test_that("length pf output is 1", {
    expect_equal(length(k_res), 1)
})

test_that("test that output for example data k = 10", {
    expect_equal(k_res, 10)
})

test_that("output is an numeric", {
    expect_equal(class(k_res), "numeric")
})

# Test for input is an rse object
test_that("getDegTx throws an error when input is not a RangedSummarizedExperiment object", {
    qsv <- list(x = matrix(seq_len(9), ncol = 3))
    expect_error(getDegTx(qsv, assayname = "tpm"), "'rse_tx' must be a RangedSummarizedExperiment object.")
})

# Test for assayname not in assayNames
test_that("k_qsvs throws an error when assayname is not in assayNames", {
    expect_error(k_qsvs(rse_tx, assayname = "not_in_assayNames"), "'not_in_assayNames' is not in assayNames\\(rse_tx\\).")
})

# Test when number of rows in 'mod' does not match number of columns in 'rse_tx'
test_that("Number of rows in 'mod' does not match number of columns in 'rse_tx'", {
    mod_not_matching <- mod
    mod_not_matching <- mod_not_matching[-1, ]
    expect_error(k_qsvs(rse_tx, mod_not_matching, "tpm"), "The number of rows in 'mod' does not match the number of input 'rse_tx' columns.")
})

test_that("non-full rank data throws error", {
    set.seed(20230621)
    expect_error(
        qSVA(
            rse_tx = rse_tx,
            sig_transcripts = select_transcripts(cell_component = TRUE),
            mod = mod2,
            assayname = "tpm"
        ),
        "matrix is not full rank"
    )
})


test_that("test that full rank matrix works correctly", {
    set.seed(20230621)
    # expect_warning(k_qsvs(rse_tx_low, mod, "tpm"), "Likely due to transcripts being not expressed in most samples")
    expect_silent(k_qsvs(rse_tx, mod, "tpm"))
})

test_that("test that mod is a matrix", {
    set.seed(20230621)
    expect_error(k_qsvs(rse_tx, mod = "mod", assayname = "tpm"), "'mod' must be a matrix.")
})