tests/testthat/test_transforming.R

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

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

testthat::test_that("transforming-se", {
  
  sacurine.se <- reading(system.file("extdata/W4M00001_Sacurine-statistics", package = "phenomis"))
  sacurine.se <- correcting(sacurine.se, figure.c = "none")
  sacurine.se <- sacurine.se[, colData(sacurine.se)[, "sampleType"] != "pool"]
  sacurine.se <- transforming(sacurine.se)
  
  testthat::expect_equal(assay(sacurine.se)["Testosterone glucuronide", "HU_neg_020"],
                         15.4297,
                         tolerance = 1e-6)
  
})

testthat::test_that("transforming-mae", {
  
  prometis.mae <- reading(system.file("extdata/prometis", package = "phenomis"))
  
  prometis.mae1 <- transforming(prometis.mae)
  testthat::expect_equivalent(assays(prometis.mae1)[["metabolomics"]]["v3", "s3"],
                              2.616842,
                              tolerance = 1e-6)
  
  prometis.mae2 <- transforming(prometis.mae, "sqrt")
  testthat::expect_equivalent(assays(prometis.mae2)[["metabolomics"]]["v3", "s3"],
                              2.476703,
                              tolerance = 1e-6)
  
})


testthat::test_that("transforming-mset", {
  
  prometis.mset <- reading(system.file("extdata/prometis", package = "phenomis"), output.c = "set")
  
  prometis.mset1 <- transforming(prometis.mset)
  testthat::expect_equal(Biobase::assayData(prometis.mset1)[["metabolomics"]][["exprs"]]["v3", "s3"],
                         2.616842,
                         tolerance = 1e-6)
  
  prometis.mset2 <- transforming(prometis.mset, "sqrt")
  testthat::expect_equal(Biobase::assayData(prometis.mset2)[["metabolomics"]][["exprs"]]["v3", "s3"],
                         2.476703,
                         tolerance = 1e-6)
  
})