tests/testthat/test_data_functions.R

In WeiSong-bio/roryk-bcbioRNASeq: RNA-Seq Utilities

context("Data Functions")



# counts =======================================================================
test_that("counts : normalized argument", {
    normalized <- list(FALSE, TRUE, "tpm", "tmm", "rlog", "vst")

    # Check that all are matrices
    expect_true(all(vapply(
        X = normalized,
        FUN = function(arg) {
            is.matrix(counts(bcb_small, normalized = arg))
        },
        FUN.VALUE = logical(1L)
    )))

    # FALSE
    expect_identical(
        counts(bcb_small, normalized = FALSE),
        assays(bcb_small)[["counts"]]
    )
    expect_identical(
        counts(bcb_small, normalized = FALSE),
        assay(bcb_small)
    )

    # TRUE
    expect_identical(
        counts(bcb_small, normalized = TRUE),
        assays(bcb_small)[["normalized"]]
    )

    # tpm
    expect_identical(
        counts(bcb_small, normalized = "tpm"),
        assays(bcb_small)[["tpm"]]
    )
    expect_identical(
        counts(bcb_small, normalized = "tpm"),
        tpm(bcb_small)
    )

    # tmm: calculated on the fly
    expect_identical(
        counts(bcb_small, normalized = "tmm"),
        tmm(bcb_small)
    )

    # rlog
    expect_identical(
        counts(bcb_small, normalized = "rlog"),
        assays(bcb_small)[["rlog"]]
    )

    # vst
    expect_identical(
        counts(bcb_small, normalized = "vst"),
        assays(bcb_small)[["vst"]]
    )
})

test_that("counts : apply transformationLimit", {
    skip <- bcb_small
    # Using `assays<-` will coerce bcbioRNASeq to SummarizedExperiment
    slot(skip, "assays")[["rlog"]] <- NULL
    slot(skip, "assays")[["vst"]] <- NULL
    expect_warning(
        counts(skip, normalized = "rlog"),
        paste(
            "rlog not present in assays.",
            "Calculating log2 TMM counts instead."
        )
    )
    expect_warning(
        counts(skip, normalized = "vst"),
        paste(
            "vst not present in assays.",
            "Calculating log2 TMM counts instead."
        )
    )
    counts <- suppressWarnings(counts(skip, normalized = "rlog"))
    expect_is(counts, "matrix")
})



# selectSamples ================================================================
test_that("selectSamples : bcbioRNASeq", {
    x <- selectSamples(bcb_small, treatment = "folic_acid")
    expect_identical(dim(x), c(500L, 3L))
    expect_identical(
        names(assays(x)),
        c("counts", "tpm", "length", "normalized", "rlog", "vst")
    )
})

test_that("selectSamples : DESeqDataSet", {
    x <- selectSamples(dds_small, treatment = "folic_acid")
    expect_identical(dim(x), c(500L, 3L))
})