context("Test: FlatLineTest() ")
data(PhyloExpressionSetExample)
nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]
test_that(
"is.ExpressionSet() throughs 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$estimate[2],
lower.tail = FALSE
)
)
})
test_that("FlatLineTest() computes correct std.dev...", {
expect_equal(sum(
FlatLineTest(
PhyloExpressionSetExample,
permutations = 1000,
custom.perm.matrix = TestBootMatrix
)$std.dev
), sum(apply(TestBootMatrix, 2, sd)))
})
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