tests/testthat/test-dim_reduction.R

In romic: R for High-Dimensional Omic Data

test_that("Removing missing values works", {
  # drop_features
  invisible(capture.output(n_features <- nrow(remove_missing_values(
    brauer_2008_triple,
    missing_val_method = "drop_features"
  )$features)))
  expect_equal(n_features, 460)

  # drop_samples with no missing samples should behave like drop_features
  invisible(capture.output(n_features <- nrow(remove_missing_values(
    brauer_2008_triple,
    missing_val_method = "drop_samples"
  )$features)))
  expect_equal(n_features, 460)

  brauer_missing_samples <- brauer_2008_triple
  brauer_missing_samples$measurements$expression[
    brauer_missing_samples$measurements$sample %in% c("G0.05", "G0.1")
  ] <- NA

  invisible(capture.output(filtered_brauer <- remove_missing_values(
    brauer_missing_samples,
    missing_val_method = "drop_samples"
  )))

  expect_equal(nrow(filtered_brauer$samples), 34)
  expect_equal(nrow(filtered_brauer$measurements), 15674)
})