tests/testthat/test-get_ic50_threshold.R

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

test_that("mhcnuggets", {
  if (!pureseqtmr::is_on_travis()) return()
  if (!mhcnuggetsr::is_mhcnuggets_installed()) return()

  expect_silent(
    get_ic50_threshold(
      peptide_length = 9,
      haplotype = get_mhc1_haplotypes()[1],
      percentile = 0.02,
      ic50_prediction_tool = "mhcnuggetsr"
    )
  )

  expect_silent(
    get_ic50_threshold(
      peptide_length = 13,
      haplotype = get_mhc2_haplotypes()[1],
      percentile = 0.02,
      ic50_prediction_tool = "mhcnuggetsr"
    )
  )
})

test_that("EpitopePrediction", {

  expect_silent(
    get_ic50_threshold(
      peptide_length = 9,
      haplotype = get_mhc1_haplotypes()[1],
      percentile = 0.02,
      ic50_prediction_tool = "EpitopePrediction"
    )
  )

  expect_error(
    get_ic50_threshold(
      peptide_length = 9,
      haplotype = get_mhc2_haplotypes()[1],
      percentile = 0.02,
      ic50_prediction_tool = "EpitopePrediction"
    )
  )
})

test_that("netmhc2pan", {

  if (!netmhc2pan::is_netmhc2pan_installed()) return()

  expect_silent(
    get_ic50_threshold(
      peptide_length = 13,
      haplotype = get_mhc2_haplotypes()[1],
      percentile = 0.02,
      ic50_prediction_tool = "netmhc2pan"
    )
  )

  expect_error(
    get_ic50_threshold(
      peptide_length = 13,
      haplotype = get_mhc1_haplotypes()[1],
      percentile = 0.02,
      ic50_prediction_tool = "netmhc2pan"
    )
  )
})