tests/testthat/test-Olink_ordinalRegression.R

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

#Load reference results
refRes_file <- '../data/refResults.RData'
load(refRes_file)

#Load data with hidden/excluded assays (all NPX=NA)
load(file = '../data/npx_data_format221010.RData')

if (requireNamespace("ordinal", quietly = TRUE) ){
#Two-way Ordinal Regression
  ordinalRegression_results <- olink_ordinalRegression(df = npx_data1,
                                                     variable="Treatment:Time") %>%
    mutate(id = as.character(OlinkID)) %>%
    arrange(id, Assay) %>% #Just for consistency. Not actually needed in this case
      select(-id)

#Posthoc
  ordinalRegression_results_posthoc_results <- olink_ordinalRegression_posthoc(npx_data1,
                                                                               variable=c("Treatment:Time"),
                                                                               olinkid_list = {ordinalRegression_results %>%
                                                                                 filter(Threshold == 'Significant' & term == 'Time') %>%
                                                                                 dplyr::select(OlinkID) %>%
                                                                                 distinct() %>%
                                                                                 pull()},
                                                                             effect = "Time") %>%
  mutate(id = as.character(OlinkID)) %>%
  arrange(id, contrast) %>% #Just for consistency. Not actually needed in this case
  select(-id)




test_that("olink_ordinalRegression works", {
  expect_equal(ordinalRegression_results, ref_results$ordinalRegression_results, tolerance = 1e-4)
  expect_error(olink_ordinalRegression(npx_data1))

  expect_warning(olink_ordinalRegression(npx_data_format221010, 'treatment2')) # data with all NPX=NA for some assays
})

test_that("olink_ordinalRegression_posthoc works", {
  expect_equal(ordinalRegression_results_posthoc_results, ref_results$ordinalRegression_results_posthoc_results)
  expect_error(olink_ordinalRegression_posthoc(df = npx_data1,
                                  variable = c('Treatment', "Time"),
                                  random = "Subject",
                                  olinkid_list = {ordinalRegression_results %>%
                                      dplyr::filter(term == 'Treatment:Time') %>%
                                      dplyr::filter(Threshold == 'Significant') %>%
                                      dplyr::pull(OlinkID)})) # no effect specified

  expect_warning(olink_ordinalRegression_posthoc(npx_data_format221010, variable = 'treatment2', effect = 'treatment2')) # data with all NPX=NA for some assays
})
}