tests/testthat/test-differentialanalysis.R

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

context("Test Differential Analysis Functions")
library("musicatk")

test_that(desc = "Diff Anal Input validity", {
  # expect_error(exposure_differential_analysis(data.frame(0)), # error here
  #             regexp = "must be a")
  data("res_annot")
  samp_annot(res_annot, "test") <- c("C", "C", "C", "B", "B", "B", "A")
  expect_error(
    exposure_differential_analysis(res_annot, "res_annot", "DNE",
      method = "wilcox"
    ),
    regexp = "does not exist"
  )
  expect_error(
    exposure_differential_analysis(res_annot, "res_annot", "test",
      method = "dummy"
    ),
    regexp = "should be one of"
  )
  expect_message(
    exposure_differential_analysis(res_annot, "res_annot", "Tumor_Subtypes",
      method = "wilcox",
      group1 = "test1",
      group2 = "test2"
    ),
    regexp = "'annotations' is of length 2."
  )
  expect_error(
    exposure_differential_analysis(res_annot, "res_annot", "test",
      method = "wilcox"
    ),
    regexp = "are required for annotations"
  )
  expect_error(
    exposure_differential_analysis(res_annot, "res_annot", "test",
      method = "wilcox",
      group1 = "test1",
      group2 = "a"
    ),
    regexp = "does not exist in annotations"
  )
  expect_error(
    exposure_differential_analysis(res_annot, "res_annot", "test",
      method = "wilcox",
      group1 = "a",
      group2 = "test1"
    ),
    regexp = "does not exist in annotations"
  )
  expect_error(
    exposure_differential_analysis(res_annot, "res_annot", "test",
      method = "wilcox",
      group1 = 1,
      group2 = "B"
    ),
    regexp = "must be character vectors"
  )
  expect_error(
    exposure_differential_analysis(res_annot, "res_annot", "test",
      method = "wilcox",
      group1 = c("A", "C"),
      group2 = "B"
    ),
    regexp = "must be the same length"
  )
  expect_error(
    exposure_differential_analysis(res_annot, "res_annot", "test",
      method = "wilcox",
      group1 = c("A", "C"),
      group2 = c("B", "C")
    ),
    regexp = "must be unique"
  )
  expect_error(
    exposure_differential_analysis(res_annot, "res_annot", "test",
      method = "wilcox",
      group1 = c("A", "t"),
      group2 = c("B", "C")
    ),
    regexp = "does not exist in annotations"
  )
  expect_error(
    exposure_differential_analysis(res_annot, "res_annot", "test",
      method = "wilcox",
      group1 = c("A", "B"),
      group2 = c("t", "C")
    ),
    regexp = "does not exist in annotations"
  )
})

test_that(desc = "Diff Anal functionality", {
  data("res_annot")
  expect_type(
    exposure_differential_analysis(res_annot, "res_annot", "Tumor_Subtypes",
      method = "wilcox"
    ),
    "list"
  )
  expect_type(
    exposure_differential_analysis(res_annot, "res_annot", "Tumor_Subtypes",
      method = "kruskal"
    ),
    "list"
  )
  expect_warning(
    exposure_differential_analysis(res_annot, "res_annot", "Tumor_Subtypes",
      method = "glm.nb"
    ),
    regexp = "NaNs produced"
  )
})