tests/testthat/test-check_inputs.R

In GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

context("Input main parameter checking works")

test_that("Early fails are triggered", {

  # providing a count matrix
  expect_error(GeneTonic(counts(dds_macrophage),
                         res_macrophage_IFNg_vs_naive,
                         res_enrich_IFNg_vs_naive,
                         annotation_obj = anno_df))

  # providing a simple data frame
  expect_error(GeneTonic(dds_macrophage,
                         deseqresult2df(res_macrophage_IFNg_vs_naive),
                         res_enrich_IFNg_vs_naive,
                         annotation_obj = anno_df))

  # providing data frame with missing key columns
  expect_error(GeneTonic(dds_macrophage,
                         res_macrophage_IFNg_vs_naive,
                         res_enrich_IFNg_vs_naive[, -1],
                         annotation_obj = anno_df))

  # providing data frame with missing key columns
  expect_error(GeneTonic(dds_macrophage,
                         res_macrophage_IFNg_vs_naive,
                         res_enrich_IFNg_vs_naive,
                         annotation_obj = anno_df[, -1]))
})

test_that("Warnings are thrown correctly", {
  expect_warning(
    checkup_GeneTonic(
      dds_unnormalized,
      res_macrophage_IFNg_vs_naive,
      res_enrich_IFNg_vs_naive,
      annotation_obj = anno_df
    )
  )

  dds_mod <- dds_macrophage[-c(1:50),]
  expect_warning(
    checkup_GeneTonic(
      dds_mod,
      res_macrophage_IFNg_vs_naive,
      res_enrich_IFNg_vs_naive,
      annotation_obj = anno_df
    )
  )


})