tests/testthat/test-RankedList.R

In acidgenomics/pfgsea: Acid Genomics GSEA

values <- eval(methodFormals(
    f = "RankedList",
    signature = "DESeqAnalysis",
    package = "AcidGSEA"
)[["value"]])

test_that("DESeqAnalysis", {
    for (value in values) {
        object <- RankedList(deseq, value = value)
        expect_s4_class(object, "RankedList")
        expect_named(
            object = object,
            expected = c("condition_B_vs_A", "treatment_D_vs_C")
        )
    }
})

rm(values)

test_that("Average values for duplicate gene symbols", {
    x <- deseq
    rowData <- rowData(x@data)
    ## Rle is subsettable with `[[`.
    ## nolint start
    rowData[["geneName"]][2L] <- rowData[["geneName"]][1L]
    rowData[["geneName"]][4L] <- rowData[["geneName"]][3L]
    ## nolint end
    rowData(x@data) <- rowData
    y <- RankedList(x)
    expect_s4_class(y, "RankedList")
})

test_that("FgseaList", {
    object <- RankedList(fgsea)
    expect_s4_class(object, "RankedList")
    expect_named(
        object = object,
        expected = c(
            "condition_B_vs_A",
            "treatment_D_vs_C"
        )
    )
})