Nothing
context("Test: EarlyConservationTest() ")
data(PhyloExpressionSetExample)
nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]
test_that(
"is.ExpressionSet() throughs error when no ExpressionSet is entered to EarlyConservationTest()",
{
expect_error(
EarlyConservationTest(
nonStandardExpressionSet,
modules = list(
early = 1:2,
mid = 3:5,
late = 6:7
),
permutations = 1000
)
)
}
)
test_that("p.value is computed..", {
expect_true(
EarlyConservationTest(
PhyloExpressionSetExample,
modules = list(
early = 1:2,
mid = 3:5,
late = 6:7
),
permutations = 1000
)$p.value > 0.9
)
})
test_that("std.dev is computed..", {
expect_true(length(
EarlyConservationTest(
PhyloExpressionSetExample,
modules = list(
early = 1:2,
mid = 3:5,
late = 6:7
),
permutations = 1000
)$std.dev
) == 7)
})
test_that("lillie.test is NA..", {
expect_true(is.na(
EarlyConservationTest(
PhyloExpressionSetExample,
modules = list(
early = 1:2,
mid = 3:5,
late = 6:7
),
permutations = 1000
)$lillie.test
))
})
test_that("lillie.test is computed...", {
skip_on_cran()
EarlyConservationTest(
PhyloExpressionSetExample,
modules = list(
early = 1:2,
mid = 3:5,
late = 6:7
),
permutations = 1000,
lillie.test = TRUE
)$lillie.test
})
test_that("error occurs when module selection does not match number of developmental stages..",
{
expect_error(
EarlyConservationTest(
PhyloExpressionSetExample,
modules = list(
early = 1:2,
mid = 3:5,
late = 6:8
),
permutations = 1000
),
"The number of stages classified into the three modules does not match the total number of stages stored in the given ExpressionSet."
)
})
test_that("error occurs when modules aren't specified...", {
expect_error(EarlyConservationTest(PhyloExpressionSetExample,
permutations = 1000))
})
test_that("EarlyConservationTest() computes correct std.dev and p.values values...",
{
skip_on_cran()
TestBootMatrix <- bootMatrix(PhyloExpressionSetExample, 1000)
res <- EarlyConservationTest(
PhyloExpressionSetExample,
modules = list(
early = 1:2,
mid = 3:5,
late = 6:7
),
custom.perm.matrix = TestBootMatrix
)
estimates <-
fitdistrplus::fitdist(apply(
TestBootMatrix,
1,
ecScore,
early = 1:2,
mid = 3:5,
late = 6:7
),
distr = "norm")
real_score <- ecScore(TAI(PhyloExpressionSetExample), 1:2, 3:5, 6:7)
expect_equal(
res$p.value,
pnorm(
real_score,
mean = estimates$estimate[1],
sd = estimates$estimate[2],
lower.tail = FALSE
)
)
expect_equal(res$std.dev, apply(TestBootMatrix , 2, sd))
})
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