tests/testthat/test-annotate.R

In RiskyCNV: Risk Analysis of Genomic Copy Number Variation

test_that("annotate returns a data frame", {
  genes_file <- system.file("extdata", "gene_annotation.csv", package = "RiskyCNV")
  cnv_file   <- system.file("extdata", "annotated_cnv.csv",   package = "RiskyCNV")

  result <- annotate(
    genes_file = genes_file,
    risk_file  = cnv_file,
    output_dir = tempdir()
  )

  expect_s3_class(result, "data.frame")
})

test_that("annotate returns correct column names", {
  genes_file <- system.file("extdata", "gene_annotation.csv", package = "RiskyCNV")
  cnv_file   <- system.file("extdata", "annotated_cnv.csv",   package = "RiskyCNV")

  result <- annotate(
    genes_file = genes_file,
    risk_file  = cnv_file,
    output_dir = tempdir()
  )

  expected_cols <- c("Sample", "GeneSymbol", "Segment_Mean", "Chr", "Start", "End")
  expect_true(all(expected_cols %in% colnames(result)))
})

test_that("annotate result has rows", {
  genes_file <- system.file("extdata", "gene_annotation.csv", package = "RiskyCNV")
  cnv_file   <- system.file("extdata", "annotated_cnv.csv",   package = "RiskyCNV")

  result <- annotate(
    genes_file = genes_file,
    risk_file  = cnv_file,
    output_dir = tempdir()
  )

  expect_true(nrow(result) > 0)
})

test_that("annotate GeneSymbol column contains character values", {
  genes_file <- system.file("extdata", "gene_annotation.csv", package = "RiskyCNV")
  cnv_file   <- system.file("extdata", "annotated_cnv.csv",   package = "RiskyCNV")

  result <- annotate(
    genes_file = genes_file,
    risk_file  = cnv_file,
    output_dir = tempdir()
  )

  expect_type(result$GeneSymbol, "character")
})

test_that("annotate saves output CSV file", {
  genes_file <- system.file("extdata", "gene_annotation.csv", package = "RiskyCNV")
  cnv_file   <- system.file("extdata", "annotated_cnv.csv",   package = "RiskyCNV")
  out_dir    <- tempdir()

  annotate(
    genes_file = genes_file,
    risk_file  = cnv_file,
    output_dir = out_dir
  )

  saved_files <- list.files(out_dir, pattern = "_annotated_", full.names = TRUE)
  expect_true(length(saved_files) > 0)
})