tests/testthat/test-stepwise-workflow.R

In RAMClustR: Mass Spectrometry Metabolomics Feature Clustering and Interpretation

test_that("RAMClustR workflow with xcms works", {
  skip_if_not_installed("xcms")
  set.seed(123) # to get reproducible results with jitters
  wd <- getwd()
  tmp <- tempdir()
  load(file.path("testdata", "test.fillpeaks"))
  expected <- readRDS(file.path("testdata", "do.findmain.rds"))
  metadata <- read_metadata(file.path("testdata", "testMetadata.csv"))
  setwd(tmp)

  ramclustObj <- rc.get.xcms.data(xcmsObj = xdata)
  ramclustObj <- rc.expand.sample.names(ramclustObj = ramclustObj, quiet = TRUE)
  ramclustObj <- rc.feature.replace.na(ramclustObj = ramclustObj)
  ramclustObj <- rc.feature.filter.blanks(ramclustObj = ramclustObj, blank.tag = "Blanc")
  ramclustObj <- rc.feature.normalize.qc(
    ramclustObj = ramclustObj,
    batch = metadata$batch,
    order = metadata$order,
    qc = metadata$qc
  )
  ramclustObj <- rc.feature.filter.cv(ramclustObj = ramclustObj)
  ramclustObj <- rc.ramclustr(ramclustObj = ramclustObj)
  ramclustObj <- rc.qc(ramclustObj = ramclustObj)
  actual <- do.findmain(ramclustObj = ramclustObj)

  # renamed phenoData colnames as test fails in R CMD checks becuase of no user input for colnames
  colnames(actual$phenoData) <- colnames(expected$phenoData)

  actual$history <- NA
  expected$history <- NA
  actual$params$rc.feature.normalize.qc <- NA
  expected$params$rc.feature.normalize.qc <- NA

  expect_equal(actual, expected)

  setwd(wd)
})