tests/testthat/test-recurrent.R

In RiskyCNV: Risk Analysis of Genomic Copy Number Variation

test_that("recurrent returns a file path as character", {
  sample_file <- system.file("extdata", "sample_data.csv", package = "RiskyCNV")
  cnv_file    <- system.file("extdata", "cnv_data.txt",    package = "RiskyCNV")

  risk_result <- classify_risk(
    file_path    = sample_file,
    column_name  = "gleason_score",
    disease_type = "prostate",
    output_dir   = tempdir()
  )

  output_path <- recurrent(
    x             = risk_result,
    risk_level    = "low_risk",
    cnv_data_file = cnv_file,
    threshold     = 2
  )

  expect_type(output_path, "character")
})

test_that("recurrent saves a readable CSV file", {
  sample_file <- system.file("extdata", "sample_data.csv", package = "RiskyCNV")
  cnv_file    <- system.file("extdata", "cnv_data.txt",    package = "RiskyCNV")

  risk_result <- classify_risk(
    file_path    = sample_file,
    column_name  = "gleason_score",
    disease_type = "prostate",
    output_dir   = tempdir()
  )

  output_path <- recurrent(
    x             = risk_result,
    risk_level    = "low_risk",
    cnv_data_file = cnv_file,
    threshold     = 2
  )

  expect_true(file.exists(output_path))

  saved_data <- read.csv(output_path)
  expected_cols <- c("Sample", "Chromosome", "Start", "End",
                     "Num_Probes", "Segment_Mean")
  expect_true(all(expected_cols %in% colnames(saved_data)))
})

test_that("recurrent throws error for invalid risk_level", {
  sample_file <- system.file("extdata", "sample_data.csv", package = "RiskyCNV")
  cnv_file    <- system.file("extdata", "cnv_data.txt",    package = "RiskyCNV")

  risk_result <- classify_risk(
    file_path    = sample_file,
    column_name  = "gleason_score",
    disease_type = "prostate",
    output_dir   = tempdir()
  )

  expect_error(
    recurrent(
      x             = risk_result,
      risk_level    = "nonexistent_risk",
      cnv_data_file = cnv_file,
      threshold     = 2
    )
  )
})