tests/testthat/test-garnish_antigens.R

In immune-health/antigen.garnish: Tumor neoantigen prediction

testthat::test_that("garnish_antigens", {
  skip_pred_tools()
  d <- test_data_dir()

  # load test data
  dt <- file.path(d, "antigen.garnish_example_output.txt") %>%
    data.table::fread() %>%
    garnish_antigens()

  # run test

  testthat::expect_equal(
    dt,
    structure(list(
      sample_id = c(
        "antigen.garnish_test_pureCN.vcf",
        "antigen.garnish_test_pureCN.vcf", "antigen.garnish_test_pureCN.vcf",
        "antigen.garnish_test_pureCN.vcf", "antigen.garnish_test_pureCN.vcf"
      ), nmer = c(
        "INNKLQQLE", "KLQQLEAAA", "LEAAAGVLE", "LQQLEAAAG",
        "NKLQQLEAA"
      ), MHC = c(
        "HLA-A*02:01", "HLA-A*02:01", "HLA-A*02:01",
        "HLA-A*02:01", "HLA-A*02:01"
      ), transcript_id = c(
        "ENST00000361445",
        "ENST00000361445", "ENST00000361445", "ENST00000361445", "ENST00000361445"
      ), protein_change = c(
        "p.Pro1426Leu", "p.Pro1426Leu", "p.Pro1426Leu",
        "p.Pro1426Leu", "p.Pro1426Leu"
      ), cDNA_change = c(
        "c.4277C>T",
        "c.4277C>T", "c.4277C>T", "c.4277C>T", "c.4277C>T"
      ), Ensemble_score = c(
        33.537419999999997,
        12.080912700000001, 5.0948799999999999, 30.55461, 10.777609999999999
      ), dissimilarity = c(0.5, NA, 0, 0.999, 0.40000000000000002),
      foreignness_score = c(
        0.66666666699999999, NA, 4.5299999999999999e-07,
        0, NA
      ), min_DAI = c(
        0.102436914, 2.5667469110000001, 14.103280010000001,
        0.13068237199999999, 11.13865477
      ), Recognition_Features = c(
        "binding affinity; foreignness; dissimilarity",
        "binding affinity", "binding affinity; foreignness; agretopicity",
        "binding affinity; dissimilarity", "binding affinity; agretopicity; dissimilarity"
      )
    ), row.names = c(NA, -5L), class = c("data.table", "data.frame"))
  )
})