tests/testthat/test-convertTranscriptsToGenes.R

In acidgenomics/r-acidexperiment: Acid Genomics Summarized Experiment

# > skip_if_not_installed("AnnotationHub")
# > skip_if_not_installed("ensembldb")
skip_if_not(hasInternet())

## NOTE Consider using a presaved object, to speed up tests.
tx2gene <- AcidGenomes::makeTxToGeneFromEnsembl(
    organism = "Homo sapiens",
    genomeBuild = "GRCh38",
    release = 87L,
    ignoreVersion = TRUE
)

test_that("character", {
    ## Ensure that function supports remapping of column names.
    t2g <- tx2gene
    colnames(t2g) <- c("x1", "x2")
    expect_identical(
        object = convertTranscriptsToGenes(
            object = c("ENST00000000233", "ENST00000000412"),
            tx2gene = t2g
        ),
        expected = factor(c(
            "ENST00000000233" = "ENSG00000004059",
            "ENST00000000412" = "ENSG00000003056"
        ))
    )
})

test_that("matrix : 'aggregate' TRUE mode", {
    object <- matrix(
        data = seq_len(8L),
        byrow = TRUE,
        nrow = 4L,
        ncol = 2L,
        dimnames = list(
            c(
                "ENST00000373020",
                "ENST00000494424",
                "ENST00000373031",
                "ENST00000485971"
            ),
            c("sample1", "sample2")
        )
    )
    expected <- matrix(
        data = c(4L, 6L, 12L, 14L),
        byrow = TRUE,
        nrow = 2L,
        ncol = 2L,
        dimnames = list(
            c("ENSG00000000003", "ENSG00000000005"),
            c("sample1", "sample2")
        )
    )
    expect_identical(
        object = convertTranscriptsToGenes(
            object = object,
            tx2gene = tx2gene,
            aggregate = TRUE
        ),
        expected = expected
    )
})

test_that("matrix : 'aggregate' FALSE mode", {
    object <- matrix(
        data = seq_len(8L),
        byrow = TRUE,
        nrow = 4L,
        ncol = 2L,
        dimnames = list(
            c(
                "ENST00000373020",
                "ENST00000494424",
                "ENST00000373031",
                "ENST00000485971"
            ),
            c("sample1", "sample2")
        )
    )
    expected <- object
    rownames(expected) <- c(
        "ENSG00000000003",
        "ENSG00000000003",
        "ENSG00000000005",
        "ENSG00000000005"
    )
    expect_identical(
        object = convertTranscriptsToGenes(
            object = object,
            tx2gene = tx2gene,
            aggregate = FALSE
        ),
        expected = expected
    )
})

test_that("Invalid params", {
    expect_error(
        object = convertTranscriptsToGenes(
            object = "ENST00000000000",
            tx2gene = tx2gene
        ),
        regexp = "ENST00000000000"
    )
    expect_error(
        object = convertTranscriptsToGenes(c("ENST00000000233", NA)),
        regexp = "isCharacter"
    )
    expect_error(
        object = convertTranscriptsToGenes(c("ENST00000000233", "")),
        regexp = "isCharacter"
    )
})

test_that("SummarizedExperiment", {
    object <- txse
    object <- convertTranscriptsToGenes(object)
    expect_s4_class(object, "SummarizedExperiment")
    expect_identical(
        object = counts(object),
        expected = matrix(
            data = c(
                15L, 18L, 21L, 24L,
                51L, 54L, 57L, 60L
            ),
            nrow = 2L,
            ncol = 4L,
            byrow = TRUE,
            dimnames = list(
                c("ENSG00000000003.15", "ENSG00000000419.12"),
                c("sample1", "sample2", "sample3", "sample4")
            )
        )
    )
})