tests/testthat/test_helper_fns.R

In pmartR/pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

context('test helper functions')

test_that('helper functions pull from correct attributes', {
  load(system.file('testdata',
    'little_seqdata.RData',
    package = 'pmartR'
  ))

  myseqData <- as.seqData(
    e_data = edata,
    f_data = fdata,
    edata_cname = 'ID_REF',
    fdata_cname = 'Samples'
  )

  expect_identical(get_data_info(myseqData), attr(myseqData, "data_info"))
  expect_identical(get_data_norm(myseqData), attr(myseqData, "data_info")$norm_info$is_normalized)
  expect_identical(get_data_scale(myseqData), attr(myseqData, "data_info")$data_scale)
  expect_identical(get_edata_cname(myseqData), attr(myseqData, "cnames")$edata_cname)
  expect_identical(get_emeta_cname(myseqData), attr(myseqData, "cnames")$emeta_cname)
  expect_identical(get_fdata_cname(myseqData), attr(myseqData, "cnames")$fdata_cname)
  expect_identical(get_meta_info(myseqData), attr(myseqData, "meta_info"))

  mes_1 <- "No filters have been applied"
  ## check after processing as well ##
  expect_null(expect_message(get_filters(myseqData), mes_1))
  expect_null(get_group_DF(myseqData))
  expect_null(get_group_table(myseqData))

  err_1 <- "object must be of class 'statRes' or 'trellData'"
  err_2 <- "dcObj object must be of class 'statRes' or 'trellData'"
  err_3 <- "omicsData must be of class 'isobaricpepData' and 'pepData'"
  err_4 <- "omicsData must be of class 'pepData', 'proData' or 'isobaricpepData'"
  err_5 <- "omicsData must be of class 'pepData', 'proData', 'metabData', 'lipidData', or 'nmrData'"
  err_6 <- "omicsData must be of class 'nmrData'"
  err_7 <- "No methods were selected for scoring, there is no 'best' set of parameters to return."

  ## Error helpers
  testthat::expect_error(get_comparisons(myseqData))
  testthat::expect_error(get_data_class(myseqData))
  testthat::expect_error(get_isobaric_info(myseqData))
  testthat::expect_error(get_isobaric_norm(myseqData))
  testthat::expect_error(get_nmr_info(myseqData))
  testthat::expect_error(get_nmr_norm(myseqData))
  testthat::expect_error(get_spans_params(myseqData))
})