tests/testthat/test_noisy_spectra.R

In powerHaDeX: Efficient Simulation of HDX-MS Data and Tools for the Statistical Analysis

test_that("get_noisy_deuteration_curves works", {
    set.seed(10)
    times <- c(5, 30, 60, 100, 500, 900)

    #pairwise grouping
    spec1 <- simulate_theoretical_spectra("PPAQHI", protection_factor = 10,
                                          charge = 1:3, times = times)
    spec2 <- simulate_theoretical_spectra("PPAQHI", protection_factor = 20,
                                          charge = 1:3, times = times)
    spec3 <- simulate_theoretical_spectra("PPAQHI", protection_factor = 30,
                                          charge = 1:3, times = times)
    spectra <- rbind(spec1, spec2, spec3)
    curves <- get_noisy_deuteration_curves(spectra,
                                           compare_pairs = TRUE,
                                           reference = "all",
                                           n_replicates = 4,
                                           n_experiments = 10)
    expect_equal(curves, readRDS("noisy_curves.RDS"))

    #all jointly
    spectra <- rbind(spec1, spec2, spec3)
    curves <- get_noisy_deuteration_curves(spectra,
                                           compare_pairs = FALSE,
                                           reference = NA,
                                           n_replicates = 4,
                                           n_experiments = 10)
    expect_equal(curves, readRDS("get_noisy_deuteration_curves_jointly.RDS"))
})


test_that("get_undeuterated_mass works", {
    spectra <- readRDS("spectra_3_states.RDS")
    expect_equal(get_undeuterated_mass(spectra), 661.35474)
})


test_that("get_spectra_list works", {
    spectra <- readRDS("spectra_3_states.RDS")

    expect_equal(get_spectra_list(spectra), readRDS("spectra_list.RDS"))
    expect_equal(get_spectra_list(spectra, compare_pairs = TRUE,
                                  reference = 'all'),
                 readRDS("spectra_list1.RDS"))
})

test_that("get_spectra_list returns error", {
    spectra <- readRDS("spectra_3_states.RDS")
    expect_error(get_spectra_list(spectra, compare_pairs = TRUE,
                                  reference = NA))
})


test_that("get_paired_spectra works", {
    spectra <- readRDS("spectra_3_states.RDS")

    #reference = 'all'
    expect_equal(get_paired_spectra(spectra, reference = 'all'),
                 readRDS("spectra_list1.RDS"))

    #reference pf is provided
    expect_error(get_paired_spectra(spectra, reference = 17),
                 "Reference protection factor does not fit the data.")
    expect_equal(get_paired_spectra(spectra, reference = 10),
                 readRDS("paired_spectra_ref_10.RDS"))
})

test_that("add_noise_to_spectra works", {
    set.seed(10)
    undeuterated_mass <- 661.35474
    spectra <- readRDS("spectra_list.RDS")
    spectra <- add_noise_to_spectra(spectra,
                                    n_replicates = 4,
                                    n_experiments = 10,
                                    undeuterated_mass,
                                    mass_deviations = 50,
                                    intensity_deviations = NULL)
    expect_equal(spectra, readRDS("spectra_noise_added.RDS"))
})

test_that("make_experimental_design works", {
    set.seed(10)
    undeuterated_mass <- 661.35474
    spectra <- readRDS("spectra_list1.RDS")
    spectra <- make_experimental_design(spectra, n_replicates = 4)

    expect_equal(spectra, readRDS("spectra_exp.RDS"))
})


test_that("make_noisy_spectra works", {
    set.seed(10)
    spectra_exp_design <- readRDS("spectra_exp.RDS")

    spectra <- make_noisy_spectra(spectra_exp_design,
                                  n_experiments = 10,
                                  undeuterated_mass = 661.35474,
                                  mass_deviations = 50,
                                  intensity_deviations = NULL)

    expect_equal(spectra, readRDS("make_noisy_spectra.RDS"))
})


test_that("add_noise_to_one_spectrum works", {
    set.seed(10)
    spectra_exp_design <- readRDS("spectra_exp.RDS")[[6]]

    spectra <- add_noise_to_one_spectrum(spectra_exp_design,
                                         undeuterated_mass = 661.35474,
                                         mass_deviations = 50,
                                         intensity_deviations = NULL)
    expect_equal(spectra, readRDS("add_noise_to_one_spectrum.RDS"))

    #intensity deviations provided
    spectra <- add_noise_to_one_spectrum(spectra_exp_design,
                                         undeuterated_mass = 661.35474,
                                         mass_deviations = 50,
                                         intensity_deviations = 0.5)
    expect_equal(spectra, readRDS("spectra_noisy_intensities.RDS"))
})


test_that("get_deuteration_curves_from_spectra works", {
    set.seed(10)
    spectra <- readRDS("spectra_noise_added.RDS")
    curves <- get_deuteration_curves_from_spectra(spectra)
    expect_equal(curves, readRDS("get_deuteration_curves_from_spectra.RDS"))
})


test_that("get_deuteration_curve_single_spectrum works", {
    set.seed(10)
    curves <- readRDS("spectra_noise_added.RDS")[[1]][[1]]
    curves <- get_deuteration_curve_single_spectrum(curves)
    expect_equal(curves, readRDS("get_deuteration_curve_single_spectrum.RDS"))
})


test_that("add_noise_to_curves works", {
    set.seed(10)
    curves <- readRDS("get_deuteration_curves_from_spectra.RDS")
    curves <- add_noise_to_curves(curves)
    expect_equal(curves, readRDS("add_noise_to_curves.RDS"))
})


test_that("add_noise_to_single_curve works", {
    set.seed(10)
    curves_data <- readRDS("get_deuteration_curves_from_spectra.RDS")[[1]][[1]]
    curves <- add_noise_to_single_curve(curves_data)
    expect_equal(curves, readRDS("add_noise_to_single_curve.RDS"))

    #provided per run deviations
    curves <- add_noise_to_single_curve(curves_data, per_run_deviations = 10)
    expect_equal(curves, readRDS("curves_per_run.RDS"))
})


test_that("fix_columns_names_types works", {
    set.seed(10)
    curves <- readRDS("add_noise_to_curves.RDS")
    curves <- fix_columns_names_types(curves)
    expect_equal(curves, readRDS("fix_columns_names_types.RDS"))
})


test_that("get_relative_mass works", {
    set.seed(10)
    mass <- rnorm(20)
    time <- 0:19
    rel_mass <- mass - mass[time == 0]
    expect_equal(rel_mass, c(0, -0.20299871301089, -1.39007672086434,
                             -0.617913886725544, 0.275798955625682,
                             0.371048129758341, -1.22682234637131,
                             -0.382422188412689, -1.64541885264492,
                             -0.275224565065818, 1.0830333321453,
                             0.737035337085511, -0.256979726960545,
                             0.968698532471564, 0.722643957441997,
                             0.0706010955539952, -0.973690027094204,
                             -0.213896555609065, 0.906775091152254,
                             0.464232353894785
    ))
})