tests/testthat/test-04_exp_design.R

In innatelab/msglm: GLM models for Mass Spectrometry Data

context("exp_design")

test_that("msglm_model()", {
  simplest_model <- msglm_model(constant_matrix(1, list(condition = "mock", effect = c())),
                                conditions = data.frame(condition = "mock"),
                                effects = data.frame(effect = character()))
  checkmate::expect_class(simplest_model, "msglm_model")
  expect_warning(msglm_model(constant_matrix(1, list(condition = "mock", effect = c())),
                             conditions = data.frame(condition = "mock"),
                             effects = data.frame(effect = character())),
                 'No effects in the experimental design')

  twoeffects_model <- msglm_model(constant_matrix(0, list(condition = "mock", effect = c("a", "b"))),
                                  conditions = data.frame(condition = "mock"),
                                  effects = data.frame(effect = c("a", "b")))
  checkmate::expect_class(twoeffects_model, "msglm_model")

  expect_warning(msglm_model(constant_matrix(0, list(condition = "mock", effect = c("a", "b"))),
                             conditions = data.frame(condition = "mock"),
                             effects = data.frame(effect = c("a", "b"))),
                 'The rank of conditionXeffect matrix \\(0\\) is lower than the number of effects \\(2\\).+')


  expect_error(msglm_model(constant_matrix(1, list(condition = "mock", effect = c("a", "a"))),
                           conditions = data.frame(condition = "mock"),
                           effects = data.frame(effect = c("a", "a"))),
               "Must have unique colnames")

  twoconditions_model <- msglm_model(constant_matrix(1, list(condition = c("mock", "b"), effect = "b")),
                                     conditions = data.frame(condition = c("mock", "b")),
                                     effects = data.frame(effect = "b"))
  checkmate::expect_class(twoconditions_model, "msglm_model")

  # check default values of effect prior
  checkmate::expect_names(colnames(twoconditions_model$effects), must.include = c("effect", "prior_mean", "prior_tau", "prior_df1", "prior_df2"))
  expect_equal(twoconditions_model$effects$prior_mean, 0.0)
  expect_equal(twoconditions_model$effects$prior_tau, 1.0)
  expect_equal(c(twoconditions_model$effects$prior_df1, twoconditions_model$effects$prior_df2), c(1.0, 1.0))

  expect_error(msglm_model(constant_matrix(1, list(condition = c(), effect = c())),
                           conditions = data.frame(condition = character()),
                           effects = data.frame(effect = character())),
               "Assertion on 'conditionXeffect' failed: Must have at least 1 rows, but has 0 rows.")
})


test_that("set_batch_effects() correctly checks the input parameters", {
  expect_error(set_batch_effects(list()), "Must inherit from class 'msglm_model'")

  simplest_model <- msglm_model(constant_matrix(1, list(condition = "mock", effect = c())),
                                conditions = data.frame(condition = "mock"),
                                effects = data.frame(effect = character()))
  simplest_model <- set_batch_effects(simplest_model, constant_matrix(1, list(msrun = "mock_1", batch_effect = "contamination")))
  checkmate::expect_class(simplest_model, "msglm_model")
})

test_that("set_contrasts() correctly checks the input parameters", {
  expect_error(set_contrasts(list()), "Must inherit from class 'msglm_model'")

  #simplest_model <- msglm_model(constant_matrix(1, list(condition = "mock", effect = c())),
   #                             conditions = data.frame(condition = "mock"),
    #                            effects = data.frame(effect = character()))
  #simplest_model <- set_batch_effects(simplest_model, constant_matrix(1, list(msrun = "mock_1", batch_effect = "contamination")))
  #checkmate::expect_class(simplest_model, "msglm_model")
})