tests/testthat/test-read_plink_map_file.R

In richelbilderbeek/plinkr: Interface to PLINK

test_that("minimal use, v1.7", {
  if (!is_plink_installed(create_plink_v1_7_options())) return()
  expect_silent(
    read_plink_map_file(
      get_plink_example_filename(
        example_filename = "test.map",
        create_plink_v1_7_options()
      )
    )
  )
})

test_that("minimal use, v1.9", {
  if (!is_plink_installed(create_plink_v1_9_options())) return()
  map_table <- read_plink_map_file(
    map_filename = get_plink_example_filename(
      example_filename = "toy.map",
      create_plink_v1_9_options()
    )
  )
  expect_silent(check_map_table(map_table))
})

test_that("use, v1.7", {
  if (!is_plink_installed(create_plink_v1_7_options())) return()
  t <- read_plink_map_file(
    get_plink_example_filename(
      example_filename = "test.map",
      create_plink_v1_7_options()
    )
  )
  expect_true("CHR" %in% names(t))
  expect_true("SNP" %in% names(t))
  expect_true("position_cm" %in% names(t))
  expect_true("BP" %in% names(t))
})

test_that("use, v1.9", {
  if (!is_plink_installed(create_plink_v1_9_options())) return()
  t <- read_plink_map_file(
    get_plink_example_filename(
      example_filename = "toy.map",
      create_plink_v1_9_options()
    )
  )
  expect_true("CHR" %in% names(t))
  expect_true("SNP" %in% names(t))
  expect_true("position_cm" %in% names(t))
  expect_true("BP" %in% names(t))
})

test_that("read and write must result in exact same file", {
  expect_equal(1 + 1, 2) # Prevents testthat warning for empty test
  # See test-save_map_table
})

test_that("use, plinkr example", {
  expect_silent(
    read_plink_map_file(
      get_plinkr_filename("random.map")
    )
  )
})