tests/testthat/test-read_plink2_psam_file.R

In richelbilderbeek/plinkr: Interface to PLINK

test_that("minimal use", {
  clear_plinkr_cache()
  expect_silent(
    read_plink2_psam_file(
      get_plinkr_filename("toy_v1_9_after_make-bed_after_make-pgen.psam")
    )
  )
  expect_silent(check_empty_plinkr_folder())
})

test_that("create, read, save, read, PLINK2", {
  if (!is_plink_installed(plink_options = create_plink_v2_0_options())) return()

  clear_plinkr_cache()
  psam_filename <- get_plinkr_filename(
    "toy_v1_9_after_make-bed_after_make-pgen.psam"
  )

  # Read the table
  psam_table <- read_plink2_psam_file(psam_filename = psam_filename)

  # Save the table
  psam_filename_again <- get_plinkr_tempfilename(fileext = ".psam")
  save_psam_table(
    psam_table = psam_table,
    psam_filename = psam_filename_again
  )

  # Read the table again
  psam_table_again <- read_plink2_psam_file(
    psam_filename = psam_filename_again
  )

  expect_identical(psam_table, psam_table_again)

  file.remove(psam_filename_again)

  expect_silent(check_empty_plinkr_folder())
})