tests/testthat/test-assoc_adjust_from_bfile.R

In richelbilderbeek/plinkr: Interface to PLINK

test_that("use", {
  clear_plinkr_cache()
  expect_silent(check_empty_plinkr_folder())

  if (!is_plink_installed()) return()
  if (!is_plink_tutorial_data_installed()) return()

  # Work in a temporary folder
  plinkr_folder <- get_plinkr_tempfilename()

  # Convert to bfile
  tutorial_data_filenames <- get_plink_tutorial_data_filenames()
  hapmap1_map_filename <- stringr::str_subset(
    tutorial_data_filenames, "hapmap1.map"
  )
  phe_filename <- stringr::str_subset(
    tutorial_data_filenames, "pop.phe"
  )

  hapmap1_base_filename <- tools::file_path_sans_ext(hapmap1_map_filename)

  base_binary_filenames <- file.path(plinkr_folder, "hapmap1")
  base_assoc_filenames <- file.path(plinkr_folder, "assoc")

  binary_filenames <- make_bed(
    base_input_filename = hapmap1_base_filename,
    base_output_filename = base_binary_filenames
  )
  if (1 == 2) {
    # Just checking
    bed_table <- read_plink_bed_file_from_files(
      bed_filename = stringr::str_subset(binary_filenames, "\\.bed$"),
      bim_filename = stringr::str_subset(binary_filenames, "\\.bim$"),
      fam_filename = stringr::str_subset(binary_filenames, "\\.fam$")
    )
  }

  bfile <- base_binary_filenames
  out <- base_assoc_filenames
  assoc_results <- assoc_adjust_from_bfile(
    bfile = base_binary_filenames,
    out = out
  )
  expect_true("assoc_table" %in% names(assoc_results))
  expect_true("assoc_adjusted_table" %in% names(assoc_results))
  expect_true("log" %in% names(assoc_results))
  list.files(dirname(base_assoc_filenames), full.names = TRUE)
  unlink(plinkr_folder, recursive = TRUE)

  expect_silent(check_empty_plinkr_folder())
  clear_plinkr_cache() # nolint
})