tests/testthat/test-aberration.R

In RiskyCNV: Risk Analysis of Genomic Copy Number Variation

test_that("aberration returns a named list", {
  cnv_file   <- system.file("extdata", "cnv_data.txt", package = "RiskyCNV")
  aberrations <- aberration(cnv_data_file = cnv_file, effect_size = 0.3)

  expect_type(aberrations, "list")
  expect_true(length(aberrations) > 0)
})

test_that("aberration list is named by chromosome number", {
  cnv_file   <- system.file("extdata", "cnv_data.txt", package = "RiskyCNV")
  aberrations <- aberration(cnv_data_file = cnv_file, effect_size = 0.3)

  # Names should be chromosome numbers as characters
  expect_true(all(grepl("^[0-9]+$", names(aberrations))))
})

test_that("aberration returns data frames with correct columns", {
  cnv_file   <- system.file("extdata", "cnv_data.txt", package = "RiskyCNV")
  aberrations <- aberration(cnv_data_file = cnv_file, effect_size = 0.3)

  expected_cols <- c("Chromosome", "Start", "End", "Num_Probes",
                     "Segment_Mean", "Sample", "Aberration", "Aberration_Code")

  for (chr in names(aberrations)) {
    expect_true(all(expected_cols %in% colnames(aberrations[[chr]])))
  }
})

test_that("aberration correctly identifies gains and losses", {
  cnv_file   <- system.file("extdata", "cnv_data.txt", package = "RiskyCNV")
  aberrations <- aberration(cnv_data_file = cnv_file, effect_size = 0.3)

  all_aberrations <- do.call(rbind, aberrations)

  # Aberration column should only contain Gain or Loss
  expect_true(all(all_aberrations$Aberration %in% c("Gain", "Loss")))

  # Aberration_Code: 1 = Gain, 0 = Loss
  expect_true(all(all_aberrations$Aberration_Code %in% c(0, 1)))
})

test_that("aberration correctly filters by effect_size threshold", {
  cnv_file   <- system.file("extdata", "cnv_data.txt", package = "RiskyCNV")
  aberrations <- aberration(cnv_data_file = cnv_file, effect_size = 0.3)

  all_aberrations <- do.call(rbind, aberrations)

  # All Gain Segment_Mean values should be > 0.3
  gains <- all_aberrations[all_aberrations$Aberration == "Gain", ]
  if (nrow(gains) > 0) {
    expect_true(all(gains$Segment_Mean > 0.3))
  }

  # All Loss Segment_Mean values should be < -0.3
  losses <- all_aberrations[all_aberrations$Aberration == "Loss", ]
  if (nrow(losses) > 0) {
    expect_true(all(losses$Segment_Mean < -0.3))
  }
})

test_that("aberration returns empty list when effect_size is very high", {
  cnv_file   <- system.file("extdata", "cnv_data.txt", package = "RiskyCNV")
  aberrations <- aberration(cnv_data_file = cnv_file, effect_size = 99)

  expect_equal(length(aberrations), 0)
})