tests/testthat/test-biascorrection.R

In rBiasCorrection: Correct Bias in DNA Methylation Analyses

prefix <- tempdir()
# prefix <- "tests/testthat/" # nolint

library(data.table)

test_that(
  desc = "correct functioning of BiasCorrection, data type 1",
  code = {

    local_edition(3)
    local_reproducible_output(rstudio = TRUE)

    plotdir <- paste0(prefix, "/plotdir/")
    csvdir <- paste0(prefix, "/csvdir/")

    b1 <- biascorrection(
      experimental = "./testdata/exp_type_1.csv",
      calibration = "./testdata/cal_type_1.csv",
      samplelocusname = "Testlocus",
      minmax = FALSE,
      correct_method = "hyperbolic",
      selection_method = "SSE",
      type = 1,
      plotdir = plotdir,
      csvdir = csvdir,
      logfilename = paste0(prefix, "/log.txt"),
      seed = 1234,
      parallel = FALSE
    )
    expect_length(list.files(plotdir), 50)
    expect_length(list.files(csvdir), 13)

    options(rBiasCorrection.nls_implementation = "GN.guess")
    b2 <- biascorrection(
      experimental = "./testdata/exp_type_1.csv",
      calibration = "./testdata/cal_type_1.csv",
      samplelocusname = "Testlocus",
      minmax = FALSE,
      correct_method = "hyperbolic",
      selection_method = "SSE",
      type = 1,
      plotdir = plotdir,
      csvdir = csvdir,
      logfilename = paste0(prefix, "/log.txt"),
      seed = 1234,
      parallel = FALSE
    )

    expect_equal(
      object = b1$final_results,
      expected = b2$final_results,
      tolerance = 1e-3
    )

    options(rBiasCorrection.nls_implementation = "LM")
    b3 <- biascorrection(
      experimental = "./testdata/exp_type_1.csv",
      calibration = "./testdata/cal_type_1.csv",
      samplelocusname = "Testlocus",
      minmax = FALSE,
      correct_method = "hyperbolic",
      selection_method = "SSE",
      type = 1,
      plotdir = plotdir,
      csvdir = csvdir,
      logfilename = paste0(prefix, "/log.txt"),
      seed = 1234,
      parallel = FALSE
    )

    expect_equal(
      object = b1$final_results,
      expected = b3$final_results,
      tolerance = 2e-1
    )
    # reset
    options(rBiasCorrection.nls_implementation = "GN.paper")

    # cleanup
    expect_silent(clean_up(plotdir = plotdir,
                           csvdir = csvdir))
    expect_true(file.remove(paste0(prefix, "/log.txt")))
})