context("Test: FlatLineTest() ")

data(PhyloExpressionSetExample)

nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]

test_that(
        "is.ExpressionSet() throws error when no ExpressionSet is entered to FlatLineTest()",
        {
                expect_error(
                        FlatLineTest(nonStandardExpressionSet,
                                     permutations = 1000)
                        )
        }
)


TestBootMatrix <- bootMatrix(PhyloExpressionSetExample, 1000)

res <- FlatLineTest(PhyloExpressionSetExample,
                    custom.perm.matrix = TestBootMatrix)

estimates <-
        fitdistrplus::fitdist(apply(TestBootMatrix, 1, var),
                              distr = "gamma",
                              method = "mme")

real_score <- var(TAI(PhyloExpressionSetExample))


test_that("FlatLineTest() computes correct p.values...", {
        expect_equal(
                FlatLineTest(
                        PhyloExpressionSetExample,
                        permutations = 1000,
                        custom.perm.matrix = TestBootMatrix
                )$p.value,
                pgamma(
                        real_score,
                        shape = estimates$estimate[1],
                        rate = estimates$estimate[2],
                        lower.tail = FALSE
                )
        , tolerance=1e-3)
})


test_that("FlatLineTest() computes correct std.dev...", {
        expect_equal(sum(
                FlatLineTest(
                        PhyloExpressionSetExample,
                        permutations = 1000,
                        custom.perm.matrix = TestBootMatrix
                )$std.dev
        ), sum(apply(TestBootMatrix, 2, sd)))
})