tests/testthat/test-correlate_with_expr.R

In RiskyCNV: Risk Analysis of Genomic Copy Number Variation

test_that("correlate_with_expr returns a named list", {
  cnv_file <- system.file("extdata", "cnv_matrix.csv", package = "RiskyCNV")
  rna_file <- system.file("extdata", "rna_data.csv",   package = "RiskyCNV")

  result <- correlate_with_expr(cnv_file = cnv_file, rna_file = rna_file)

  expect_type(result, "list")
  expect_true(all(c("all_correlations", "significant", "high_correlation") %in%
                    names(result)))
})

test_that("correlate_with_expr all_correlations has correct columns", {
  cnv_file <- system.file("extdata", "cnv_matrix.csv", package = "RiskyCNV")
  rna_file <- system.file("extdata", "rna_data.csv",   package = "RiskyCNV")

  result <- correlate_with_expr(cnv_file = cnv_file, rna_file = rna_file)

  expected_cols <- c("gene", "cor_val", "p.value")
  expect_true(all(expected_cols %in% colnames(result$all_correlations)))
})

test_that("correlate_with_expr finds common genes", {
  cnv_file <- system.file("extdata", "cnv_matrix.csv", package = "RiskyCNV")
  rna_file <- system.file("extdata", "rna_data.csv",   package = "RiskyCNV")

  result <- correlate_with_expr(cnv_file = cnv_file, rna_file = rna_file)

  expect_true(nrow(result$all_correlations) > 0)
})

test_that("correlate_with_expr correlation values are between -1 and 1", {
  cnv_file <- system.file("extdata", "cnv_matrix.csv", package = "RiskyCNV")
  rna_file <- system.file("extdata", "rna_data.csv",   package = "RiskyCNV")

  result <- correlate_with_expr(cnv_file = cnv_file, rna_file = rna_file)

  expect_true(all(result$all_correlations$cor_val >= -1 &
                    result$all_correlations$cor_val <= 1))
})

test_that("correlate_with_expr p.values are between 0 and 1", {
  cnv_file <- system.file("extdata", "cnv_matrix.csv", package = "RiskyCNV")
  rna_file <- system.file("extdata", "rna_data.csv",   package = "RiskyCNV")

  result <- correlate_with_expr(cnv_file = cnv_file, rna_file = rna_file)

  expect_true(all(result$all_correlations$p.value >= 0 &
                    result$all_correlations$p.value <= 1))
})

test_that("correlate_with_expr significant subset has p.value < 0.05", {
  cnv_file <- system.file("extdata", "cnv_matrix.csv", package = "RiskyCNV")
  rna_file <- system.file("extdata", "rna_data.csv",   package = "RiskyCNV")

  result <- correlate_with_expr(cnv_file = cnv_file, rna_file = rna_file)

  if (nrow(result$significant) > 0) {
    expect_true(all(result$significant$p.value < 0.05))
  }
})

test_that("correlate_with_expr high_correlation subset has cor_val > 0.8", {
  cnv_file <- system.file("extdata", "cnv_matrix.csv", package = "RiskyCNV")
  rna_file <- system.file("extdata", "rna_data.csv",   package = "RiskyCNV")

  result <- correlate_with_expr(cnv_file = cnv_file, rna_file = rna_file)

  if (nrow(result$high_correlation) > 0) {
    expect_true(all(result$high_correlation$cor_val > 0.8))
    expect_true(all(result$high_correlation$p.value < 0.05))
  }
})