tests/testthat/test_peak_area.R

In shubham1637/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

test_that("test_calculateIntensity", {
  time <- c( 2.23095,2.239716667,2.248866667,2.25765,2.266416667,
             2.275566667,2.2847,2.293833333,2.304066667,2.315033333,2.325983333,2.336566667,
             2.3468,2.357016667,2.367283333,2.377183333,2.387083333,2.39735,2.40725,2.4175,
             2.4274,2.4373,2.44755,2.45745,2.4677,2.477966667,2.488216667,2.498516667,2.5084,
             2.5183,2.5282,2.538466667,2.548366667,2.558266667,2.568516667,2.578783333,
             2.588683333,2.59895,2.6092,2.619466667,2.630066667,2.64065,2.65125,2.662116667,
             2.672716667,2.6833,2.6939,2.7045,2.715083333,2.725683333,2.736266667,2.746866667,
             2.757833333,2.768416667,2.779016667,2.789616667,2.8002,2.810116667,2.820033333,
             2.830316667,2.840216667,2.849766667,2.859316667,2.868866667,2.878783333,2.888683333,
             2.898233333,2.907783333,2.916033333,2.924266667,2.93215,2.940383333,2.947933333,
             2.955816667,2.964066667,2.97195,2.979833333,2.987716667,2.995616667,3.003516667,
             3.011416667,3.01895,3.026833333,3.034366667,3.042266667,3.0498,3.05735,3.065233333,
             3.073133333,3.080666667,3.0882,3.095733333,3.103633333,3.111533333,3.119066667,
             3.126966667,3.134866667,3.14275,3.15065,3.15855,3.166433333,3.174333333,3.182233333,
             3.190133333,3.198016667,3.205916667,3.213166667
  )

  intensity <- c(
    1447,2139,1699,755,1258,1070,944,1258,1573,1636,
    1762,1447,1133,1321,1762,1133,1447,2391,692,1636,2957,1321,1573,1196,1258,881,
    1384,2076,1133,1699,1384,692,1636,1133,1573,1825,1510,2391,4342,10382,17618,
    51093,153970,368094,632114,869730,962547,966489,845055,558746,417676,270942,
    184865,101619,59776,44863,31587,24036,20450,20324,11074,9879,10508,7928,7110,
    6733,6481,5726,6921,6670,5537,4971,4719,4782,5097,5789,4279,5411,4530,3524,
    2139,3335,3083,4342,4279,3083,3649,4216,4216,3964,2957,2202,2391,2643,3524,
    2328,2202,3649,2706,3020,3335,2580,2328,2894,3146,2769,2517
  )
  df <- data.frame(time, intensity)
  left <- 2.472833334
  right <- 3.022891666
  params <- paramsDIAlignR()
  params[["baseSubtraction"]] <- TRUE
  outData <- calculateIntensity(list(df), left, right, params)
  expect_equal(outData, 6645331.33866)

  df <- cbind(time, intensity)
  outData <- calculateIntensity(list(df), left, right, params)
  expect_equal(outData, 6645331.33866)

  params$baselineType <- "vertical_division_min"; params$integrationType <- "trapezoid"
  outData <- calculateIntensity(list(df, df), left, right, params)
  expect_equal(outData, 2*71063.59368, tolerance = 0.01)

  params$transitionIntensity <- TRUE
  outData <- calculateIntensity(list(df, df), left, right, params)
  expect_equal(outData, rep(71063.59368, 2), tolerance = 0.01)

  params$smoothPeakArea <- TRUE
  outData <- calculateIntensity(list(df, df), left, right, params)
  expect_equal(outData, rep(70842.3, 2), tolerance = 0.01)
})


test_that("test_recalculateIntensity", {
  peakTable <- data.table(precursor = c(1967L, 1967L, 2474L, 2474L),
                          run = rep(c("hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt",
                      "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"), 2),
                      intensity = c(186.166, 579.832, 47.9525, 3.7413),
                      leftWidth = c(5001.76, 5025.66, 6441.51, 6516.6),
                      rightWidth = c(5076.86, 5121.25, 6475.65, 6554.2))
  dataPath <- system.file("extdata", package = "DIAlignR")
  outData <- recalculateIntensity(peakTable, dataPath)
  expOutput <- data.table(precursor = c(1967L, 1967L, 2474L, 2474L),
                          run = rep(c("hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt",
                                      "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"), 2),
                          intensity = c(186.166288, 582.069568, 49.424775, 7.380512),
                          leftWidth = c(5001.76, 5025.66, 6441.51, 6516.6),
                          rightWidth = c(5076.86, 5121.25, 6475.65, 6554.2),
                          key="precursor")
  expect_equal(outData, expOutput, tolerance = 1e-05)
})



test_that("test_reIntensity", {
  data(multipeptide_DIAlignR, package="DIAlignR")
  data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR, package="DIAlignR")
  params <- paramsDIAlignR()
  params[["baseSubtraction"]] <- TRUE
  XICs.eXp <- list()
  df <- data.table::data.table(multipeptide_DIAlignR[["14383"]])
  XICs.eXp[["4618"]] <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]]

  reIntensity(df, "run2", XICs.eXp, params)
  expect_equal(df[5,intensity], 255.496)

  df[5, alignment_rank:= 1L]
  reIntensity(df, "run2", XICs.eXp, params)
  expect_equal(df[5L, intensity], 211.3709, tolerance = 1e-05)

  dataPath <- system.file("extdata", package = "DIAlignR")
  mz <- mzR::openMSfile(file.path(dataPath, "xics","hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML"))
  df <- data.table::data.table(multipeptide_DIAlignR[["9861"]])
  chromIndices <- list(c(43, 44, 45, 46, 47, 48), c(49, 50, 51, 52, 53, 54))
  XICs.eXp <- lapply(chromIndices, function(i) extractXIC_group(mz, chromIndices = i))
  names(XICs.eXp) <- c("9719", "9720")

  df$alignment_rank[c(6L,10L)] <- 1L
  reIntensity(df, "run2", XICs.eXp, params)
  expect_equal(df[6L, intensity], 52.95950)
  expect_equal(df[10L, intensity], 24.50702, tolerance = 1e-05)

  mz <- mzR::openMSfile(file.path(dataPath, "xics","hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML"))
  XICs.ref <- lapply(chromIndices, function(i) extractXIC_group(mz, chromIndices = i))
  names(XICs.ref) <- c("9719", "9720")

  reIntensity(df, "run1", XICs.ref, params)
  expect_equal(df[6L, intensity], 20.11727)
})