context("Test : tfStability() ")
data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)
equal_df <- function(df1, df2) {
rownames(df1) <- NULL
rownames(df2) <- NULL
isTRUE(all.equal(df1, df2))
}
nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]
test_that("is.ExpressionSet() throws error when no ExpressionSet is entered to tfStability()",
{
expect_error(
tfStability(nonStandardExpressionSet)
)
})
test_that("tfStability() throws error when an unavailable TestStatistic is entered to tfStability()",
{
expect_error(
tfStability(PhyloExpressionSetExample, TestStatistic = "WavyLineTest")
)
})
test_that("tfStability() throws error when modules are not specified",
{
expect_error(
tfStability(PhyloExpressionSetExample, TestStatistic = "ReductiveHourglassTest")
)
})
test_that("error occurs when module selection does not match number of developmental stages..",
{
expect_error(
tfStability(PhyloExpressionSetExample,
TestStatistic = "ReductiveHourglassTest",
modules = list(
early = 1:2,
mid = 3:5,
late = 6:8))
)
})
test_that("error occurs when transformation is not available",
{
expect_error(
tfStability(PhyloExpressionSetExample,
TestStatistic = "ReductiveHourglassTest",
transforms = c("rank", "sqwuared"),
modules = list(
early = 1:2,
mid = 3:5,
late = 6:7),
permutations = 100)
)
})
test_that("tfStability() computes correct p-values ", {
expect_true(tfStability(ExpressionSet = PhyloExpressionSetExample,
TestStatistic = "ReductiveHourglassTest",
transforms = c("log2", "sqrt", "none"),
modules = list(early = 1:2, mid = 3:5, late = 6:7),
permutations = 100)[2] < 0.05
)
})
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