tests/testthat/test_correcting.R

In SciDoPhenIA/phenomis: Analysis of single and multiple phenomic data sets

testthat::context("Testing 'correcting'")

testthat::test_that("correcting-se", {
  
  sacurine.se <- reading(system.file("extdata/W4M00001_Sacurine-statistics", package = "phenomis"))
  sacurine.se <- correcting(sacurine.se, method.vc = "loess")
  
  testthat::expect_equal(assay(sacurine.se)["Testosterone glucuronide", "HU_neg_020"],
                         44136.83,
                         tolerance = 1e-6)
  
})

testthat::test_that("correcting-mae", {
  
  sacurine.se <- reading(system.file("extdata/W4M00001_Sacurine-statistics", package = "phenomis"))
  sac_map.df <- data.frame(primary = colnames(sacurine.se),
                           colname = colnames(sacurine.se))
  map.ls <- list(sac1 = sac_map.df,
                 sac2 = sac_map.df)
  map.df <- MultiAssayExperiment::listToMap(map.ls)
  sac.mae <- MultiAssayExperiment::MultiAssayExperiment(experiments = list(sac1 = sacurine.se,
                                                                           sac2 = sacurine.se),
                                                        colData = colData(sacurine.se),
                                                        sampleMap = map.df)
  sac.mae <- correcting(sac.mae, method.vc = c("loess", "serrf"))
  
  testthat::expect_equal(assays(sac.mae)[["sac1"]]["Testosterone glucuronide", "HU_neg_020"],
                         44136.83,
                         tolerance = 1e-6)
  
  testthat::expect_equal(assays(sac.mae)[["sac2"]]["Testosterone glucuronide", "HU_neg_020"],
                         64660.22,
                         tolerance = 1e-6)
  
  
})