tests/testthat/test_rmd_conversion.R

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

context('RMD conversion')

test_that('conversion between log2(RMD) and p-values is seamless', {
  # Load data and prepare omicsData objects ------------------------------------

  load(system.file('testdata',
    'metaboliteData.RData',
    package = 'pmartR'
  ))

  mdata <- as.metabData(
    e_data = edata,
    f_data = fdata,
    e_meta = emeta,
    edata_cname = 'Metabolite',
    fdata_cname = 'SampleID',
    emeta_cname = 'MClass'
  )

  mdata <- edata_transform(
    omicsData = mdata,
    data_scale = "log"
  )

  mdata <- group_designation(
    omicsData = mdata,
    main_effects = "Condition"
  )

  # Holy RMD conversion tests, Batman! -----------------------------------------

  rmd_filta <- rmd_filter(
    omicsData = mdata,
    metrics = c("MAD", "Skewness", "Correlation")
  )

  expect_identical(
    rmd_conversion(log2rmd = rmd_filta$Log2.md, df = 3),
    1 - pchisq(2^(rmd_filta$Log2.md), df = 3)
  )

  expect_identical(
    rmd_conversion(pval = .0001, df = 5),
    log(qchisq(1 - 0.0001, df = 5), base = 2)
  )

  expect_identical(
    rmd_conversion(log2rmd = 4.5, df = 3),
    1 - pchisq(2^(4.5), df = 3)
  )
})