tests/testthat/test-CombinatorialSignificance.R

In myTAI: Evolutionary Transcriptomics

context("Test: CombinatorialSignificance() ")

data(PhyloExpressionSetExample)


nonStandardExpressionSet <- PhyloExpressionSetExample[ , 2:9]

test_that(
        "is.ExpressionSet() throughs error when no ExpressionSet is entered to CombinatorialSignificance()",
        {
                expect_error(
                        CombinatorialSignificance(
                                ExpressionSet = nonStandardExpressionSet,
                                replicates    = c(2, 3, 2),
                                TestStatistic = "FlatLineTest",
                                permutations  = 10,
                                parallel      = FALSE
                        )
                )
        }
)

test_that("variable and constant replicate values for corresponding stages work properly..",
          {
                  expect_equal(length(
                          CombinatorialSignificance(
                                  ExpressionSet = PhyloExpressionSetExample,
                                  replicates    = c(2, 3, 2),
                                  TestStatistic = "FlatLineTest",
                                  permutations  = 10,
                                  parallel      = FALSE
                          )
                  ), prod(c(2, 3, 2)))
                  
                  expect_equal(length(
                          CombinatorialSignificance(
                                  ExpressionSet = PhyloExpressionSetExample,
                                  replicates    = c(3, 1, 3),
                                  TestStatistic = "FlatLineTest",
                                  permutations  = 10,
                                  parallel      = FALSE
                          )
                  ), prod(c(3, 1, 3)))
                  
                  expect_equal(length(
                          CombinatorialSignificance(
                                  ExpressionSet = PhyloExpressionSetExample[ , 1:8],
                                  replicates    = 2,
                                  TestStatistic = "FlatLineTest",
                                  permutations  = 10,
                                  parallel      = FALSE
                          )
                  ), 8)
                  
                  #         expect_error(CombinatorialSignificance(ExpressionSet = PhyloExpressionSetExample,
                  #                                                replicates    = c(0,3,4),
                  #                                                TestStatistic = "FlatLineTest",
                  #                                                permutations  = 10,
                  #                                                parallel      = FALSE))
                  
          })


test_that("Error occurs in case a TestStatistic other than FlatLineTest has been chosen...",
          {
                  expect_error(
                          CombinatorialSignificance(
                                  ExpressionSet = PhyloExpressionSetExample,
                                  replicates    = c(2, 3, 2),
                                  TestStatistic = "ReductiveHourglassTets",
                                  permutations  = 10,
                                  parallel      = FALSE
                          ),
                          "Please enter a correct string for the test statistic: 'FlatLineTest'."
                  )
          })