tests/testthat/test_get_global_fit.R

In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

context("Global Fit")

test_that("test_getLOESSfit", {
  data(oswFiles_DIAlignR, package="DIAlignR")
  oswFiles <- oswFiles_DIAlignR
  Loess.fit <- getLOESSfit(oswFiles, ref = "run1", eXp = "run2", maxFdrGlobal = 0.05, spanvalue = 0.1)
  # Testing for Residual standard error
  expect_equal(Loess.fit$s, 22.23519, tolerance = 1e-05)
  # Add predict function as well.
  expect_equal(predict(Loess.fit, newdata = data.frame("RT.ref"= 4978.4))[[1]], 4964.752, tolerance = 1e-05)
  expect_equal(predict(Loess.fit, newdata = data.frame("RT.ref"= 5575.8))[[1]], 5565.462, tolerance = 1e-05)
})

test_that("test_getLinearfit", {
  data(oswFiles_DIAlignR, package="DIAlignR")
  oswFiles <- oswFiles_DIAlignR
  Linear.fit <- getLinearfit(oswFiles, ref = "run1", eXp = "run2", maxFdrGlobal = 0.05)
  # Testing for Residual standard error
  expect_equal(summary(Linear.fit)[["sigma"]], 30.12705, tolerance = 1e-05)
  outData <- predict(Linear.fit, newdata = data.frame("RT.ref"=4978.4))[[1]]
  expect_equal(outData, 4990.682, tolerance = 1e-05)
  outData <- predict(Linear.fit, newdata = data.frame("RT.ref"=5575.8))[[1]]
  expect_equal(outData, 5577.561, tolerance = 1e-05)
})

test_that("test_getGlobalAlignment", {
  data(oswFiles_DIAlignR, package="DIAlignR")
  oswFiles <- oswFiles_DIAlignR
  globalFit <- getGlobalAlignment(oswFiles, ref = "run1", eXp = "run2", maxFdrGlobal = 0.05, spanvalue = 0.1, fitType = "loess")
  # Testing for Residual standard error
  expect_equal(globalFit$s, 22.23519, tolerance = 1e-05)
  # Add predict function as well.
  expect_equal(predict(globalFit, newdata = data.frame("RT.ref"= 4978.4))[[1]], 4964.752, tolerance = 1e-05)
  expect_equal(predict(globalFit, newdata = data.frame("RT.ref"= 5575.8))[[1]], 5565.462, tolerance = 1e-05)

  globalFit <- getGlobalAlignment(oswFiles, ref = "run1", eXp = "run2", maxFdrGlobal = 0.05, fitType = "linear")
  # Testing for Residual standard error
  expect_equal(summary(globalFit)[["sigma"]], 30.12705, tolerance = 1e-05)
  outData <- predict(globalFit, newdata = data.frame("RT.ref"=4978.4))[[1]]
  expect_equal(outData, 4990.682, tolerance = 1e-05)
  outData <- predict(globalFit, newdata = data.frame("RT.ref"=5575.8))[[1]]
  expect_equal(outData, 5577.561, tolerance = 1e-05)
})


test_that("test_getRSE", {
  data(oswFiles_DIAlignR, package="DIAlignR")
  oswFiles <- oswFiles_DIAlignR
  globalFit <- getGlobalAlignment(oswFiles, ref = "run1", eXp = "run2", maxFdrGlobal = 0.05, spanvalue = 0.1, fitType = "loess")
  expect_equal(getRSE(globalFit), 22.23519, tolerance = 1e-05)

  globalFit <- getGlobalAlignment(oswFiles, ref = "run1", eXp = "run2", maxFdrGlobal = 0.05, fitType = "linear")
  expect_equal(getRSE(globalFit), 30.12705, tolerance = 1e-05)
})


test_that("test_getGlobalFits", {
  dataPath <- system.file("extdata", package = "DIAlignR")
  fileInfo <- getRunNames(dataPath, oswMerged = TRUE)
  features <- getFeatures(fileInfo, maxFdrQuery = 0.05)
  refRun <- data.frame("transition_group_id" = c(32L, 18342L),
                       "run" = c("run0", "run1"),stringsAsFactors = FALSE)
  globalFits <- getGlobalFits(refRun, features, fileInfo, "loess", 0.05, 0.1)
  globalFit <- globalFits[["run1_run2"]]
  expect_equal(globalFit$s, 22.23519, tolerance = 1e-05)

  globalFits <- getGlobalFits(refRun, features, fileInfo, "linear", 0.05, 0.1)
  globalFit <- globalFits[["run1_run2"]]
  expect_equal(summary(globalFit)[["sigma"]], 30.12705, tolerance = 1e-05)
})