tests/testthat/test-preprocess_functions.R

In russHyde/miiq: Microarrays Are Awesome: Get Them Analysed HERE!

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context("Test preprocess functions")

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.df <- function(...) {
  data.frame(..., stringsAsFactors = FALSE, check.names = FALSE)
}

test_that("we can add an entrez.id and symbol to an ExpressionSet", {
  eset <- random_eset(
    n_probes = 5,
    n_samples = 2,
    features = .df(
      `Gene ID` = as.character(1:5),
      `Gene symbol` = c("ABC///DEF", "EEE///EEE", LETTERS[3:5])
    )
  )

  expect_true(
    all(
      c("entrez.id", "symbol") %in%
        colnames(
          Biobase::featureData(
            add_entrez_columns_if_gset_has_annotgpl(eset))))
  )
  expect_equal(
    Biobase::fData(add_entrez_columns_if_gset_has_annotgpl(eset))$entrez.id,
    as.character(1:5)
  )
  expect_equal(
    Biobase::fData(add_entrez_columns_if_gset_has_annotgpl(eset))$symbol,
    c("ABC|DEF", "EEE", LETTERS[3:5])
  )
})