tests/testthat/test-peak_detection.R

In sipss/AlpsNMR: Automated spectraL Processing System for NMR

test_that("nmr_detect_peaks & nmr_align_find_ref & nmr_align & nmr_integrate_peak_position works", {
    dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR")
    dataset <- nmr_read_samples_dir(dir_to_demo_dataset)
    data2 <- dataset[1:3]
    dataset <- nmr_interpolate_1D(dataset, axis = c(min = 1, max = 2, by = 0.002))
    dataset <- nmr_baseline_estimation(dataset)

    peak_table <- nmr_detect_peaks(dataset,
        nDivRange_ppm = 0.1,
        scales = seq(1, 16, 2),
        baselineThresh = 1e+03, SNR.Th = 2
    )
    NMRExp_ref <- nmr_align_find_ref(dataset, peak_table)
    dataset <- nmr_align(dataset,
        peak_table,
        NMRExp_ref,
        maxShift_ppm = 0.0015,
        acceptLostPeak = FALSE
    )

    plot <- nmr_detect_peaks_plot(dataset, peak_table, NMRExp_ref)


    peak_table_integration <- nmr_integrate_peak_positions(
        samples = dataset,
        peak_pos_ppm = list(c(2, 3, 4)),
        peak_width_ppm = NULL
    )
    expect_true(is.list(data2[["data_1r"]]))
    expect_true(is.numeric(peak_table_integration[["peak_table"]][[1]]))
    expect_true(is.integer(dim(peak_table)))
    expect_true(is.character(NMRExp_ref))
    expect_true(is.list(plot[1]))
    expect_true(is.matrix(dataset[["data_1r"]]))
    expect_true(is.numeric(dataset[["data_1r"]][[1]]))
})

test_that("nmr_integrate_regions works", {
    dataset <- new_nmr_dataset_1D(
        ppm_axis = 1:10,
        data_1r = matrix(sample(0:99, replace = TRUE), nrow = 10),
        metadata = list(external = data.frame(NMRExperiment = c("10", "20", "30", "40", "50", "60", "70", "80", "90", "100")))
    )
    peak_table_integration <- nmr_integrate_regions(
        samples = dataset,
        regions = list(random = c(2, 5)),
        fix_baseline = TRUE
    )
    expect_true(is.matrix(peak_table_integration[["peak_table"]]))
    expect_true(is.numeric(peak_table_integration[["peak_table"]][[1]]))
})