validate_nmr_dataset_peak_table {AlpsNMR} | R Documentation

## Validate nmr_dataset_peak_table objects

### Description

The function detects peaks on an nmr_dataset_1D object, using speaq::detectSpecPeaks. `detectSpecPeaks` divides the whole spectra into smaller segments and uses MassSpecWavelet::peakDetectionCWT for peak detection.

This function is based on speaq::dohCluster.

The function allows the integration of a given ppm vector with a specific width.

### Usage

    validate_nmr_dataset_peak_table(nmr_dataset_peak_table)

    nmr_detect_peaks(
      nmr_dataset,
      nDivRange_ppm = 0.1,
      scales = seq(1, 16, 2),
      baselineThresh = NULL,
      SNR.Th = 3
    )

    nmr_detect_peaks_plot(nmr_dataset, peak_data, NMRExperiment, ...)

    nmr_detect_peaks_tune_snr(
      ds,
      NMRExperiment = NULL,
      SNR_thresholds = seq(from = 2, to = 6, by = 0.1)
    )

    nmr_align(
      nmr_dataset,
      peak_data,
      NMRExp_ref = NULL,
      maxShift_ppm = 0.0015,
      acceptLostPeak = FALSE
    )

    nmr_integrate_peak_positions(
      samples,
      peak_pos_ppm,
      peak_width_ppm = 0.006,
      ...
    )

    get_integration_with_metadata(integration_object)

### Arguments

`nmr_dataset_peak_table` | An nmr_dataset_peak_table object
`nmr_dataset` | An nmr_dataset_1D
`nDivRange_ppm` | Segment size, in ppms, to divide the spectra and search for peaks.
`scales` | The parameter of peakDetectionCWT function of MassSpecWavelet package, look it up in the original function.
`baselineThresh` | It will remove all peaks under an intensity set by baselineThresh. If you set it to 'NULL', nmr_detect_peaks will automatically compute an aproximate value considering baseline between 9.5 and 10.0 ppm (automatically calculation using `baselineThresh = NULL` will not work if spectra were not interpolated up to 10.0 ppm)
`SNR.Th` | The parameter of peakDetectionCWT function of MassSpecWavelet package, look it up in the original function. If you set -1, the function will itself re-compute this value.
`peak_data` | The detected peak data given by nmr_detect_peaks.
`NMRExperiment` | A string with the single NMRExperiment used explore the SNR thresholds. If not given, use the first one.
`...` | Arguments passed on to `nmr_integrate_regions` `regions` A named list. Each element of the list is a region, given as a named numeric vector of length two with the range to integrate. The name of the region will be the name of the column
`ds` | An nmr_dataset_1D dataset
`SNR_thresholds` | A numeric vector with the SNR thresholds to explore
`NMRExp_ref` | NMRExperiment of the reference to use for alignment
`maxShift_ppm` | The maximum shift allowed, in ppm
`acceptLostPeak` | This is an option for users, TRUE is the default value. If the users believe that all the peaks in the peak list are true positive, change it to FALSE.
`samples` | A nmr_dataset object
`peak_pos_ppm` | The peak positions, in ppm
`peak_width_ppm` | The peak widths (or a single peak width for all peaks)
`integration_object` | A nmr_dataset object

### Value

The nmr_dataset_peak_table unchanged

This function is useful for its side-effects: Stopping in case of error

A data frame with the NMRExperiment, the sample index, the position in ppm and index and the peak intensity

Plot peak detection results

A list with the following elements:

- `peaks_detected`: A data frame with the columns from the nmr_detect_peaks output and an additional column `SNR_threshold` with the threshold used on each row.

- `num_peaks_per_region`: A summary of the `peaks_detected` table, with the number of peaks detected on each chemical shift region

- `plot_num_peaks_per_region`: A visual representation of `num_peaks_per_region`

- `plot_spectrum_and_detections`: A visual representation of the spectrum and the peaks detected with each SNR threshold. Use plotly::ggplotly or plot_interactive on this to zoom and explore the results.

An nmr_dataset_1D, with the spectra aligned

Integrate peak positions

Get integrals with metadata from `integrate peak positions`

integration dataframe

### Parallelization

This function accepts parallellization with future strategies. You can use `plan(multiprocess)` or `plan(sequential)` before calling this function to determine if it should be parallellized or not.

### See Also

nmr_align for peak alignment with the detected peak table

Other nmr_dataset_peak_table functions: `[.nmr_dataset_peak_table()`, `format.nmr_dataset_peak_table()`, `is.nmr_dataset_peak_table()`, `load_and_save_functions`, `new_nmr_dataset_peak_table()`, `nmr_meta_add()`, `nmr_meta_export()`, `nmr_meta_get_column()`, `nmr_meta_get()`, `print.nmr_dataset_peak_table()`

Other class helper functions: `format.nmr_dataset_1D()`, `format.nmr_dataset_peak_table()`, `format.nmr_dataset()`, `is.nmr_dataset_1D()`, `is.nmr_dataset_peak_table()`, `new_nmr_dataset_1D()`, `new_nmr_dataset_peak_table()`, `new_nmr_dataset()`, `print.nmr_dataset_1D()`, `print.nmr_dataset_peak_table()`, `print.nmr_dataset()`, `validate_nmr_dataset_family()`, `validate_nmr_dataset()`

Other peak detection functions: `Pipelines`, `nmr_baseline_threshold()`, `nmr_identify_regions_blood()`, `nmr_identify_regions_cell()`, `nmr_identify_regions_urine()`, `nmr_integrate_regions()`, `regions_from_peak_table()`

Other nmr_dataset_1D functions: `[.nmr_dataset_1D()`, `computes_peak_width_ppm()`, `file_lister()`, `files_to_rDolphin()`, `format.nmr_dataset_1D()`, `is.nmr_dataset_1D()`, `load_and_save_functions`, `new_nmr_dataset_1D()`, `nmr_align_find_ref()`, `nmr_baseline_removal()`, `nmr_baseline_threshold()`, `nmr_exclude_region()`, `nmr_integrate_regions()`, `nmr_interpolate_1D()`, `nmr_meta_add()`, `nmr_meta_export()`, `nmr_meta_get_column()`, `nmr_meta_get()`, `nmr_normalize()`, `nmr_pca_build_model()`, `nmr_pca_outliers_filter()`, `nmr_pca_outliers_plot()`, `nmr_pca_outliers_robust()`, `nmr_pca_outliers()`, `nmr_ppm_resolution()`, `plot.nmr_dataset_1D()`, `plot_webgl()`, `print.nmr_dataset_1D()`, `rdCV_PLS_RF_ML()`, `rdCV_PLS_RF()`, `save_files_to_rDolphin()`, `to_ChemoSpec()`, `validate_nmr_dataset()`

Other peak detection functions: `Pipelines`, `nmr_baseline_threshold()`, `nmr_identify_regions_blood()`, `nmr_identify_regions_cell()`, `nmr_identify_regions_urine()`, `nmr_integrate_regions()`, `regions_from_peak_table()`

Other peak detection functions: `Pipelines`, `nmr_baseline_threshold()`, `nmr_identify_regions_blood()`, `nmr_identify_regions_cell()`, `nmr_identify_regions_urine()`, `nmr_integrate_regions()`, `regions_from_peak_table()`

Other nmr_dataset_1D functions: `[.nmr_dataset_1D()`, `computes_peak_width_ppm()`, `file_lister()`, `files_to_rDolphin()`, `format.nmr_dataset_1D()`, `is.nmr_dataset_1D()`, `load_and_save_functions`, `new_nmr_dataset_1D()`, `nmr_align_find_ref()`, `nmr_baseline_removal()`, `nmr_baseline_threshold()`, `nmr_exclude_region()`, `nmr_integrate_regions()`, `nmr_interpolate_1D()`, `nmr_meta_add()`, `nmr_meta_export()`, `nmr_meta_get_column()`, `nmr_meta_get()`, `nmr_normalize()`, `nmr_pca_build_model()`, `nmr_pca_outliers_filter()`, `nmr_pca_outliers_plot()`, `nmr_pca_outliers_robust()`, `nmr_pca_outliers()`, `nmr_ppm_resolution()`, `plot.nmr_dataset_1D()`, `plot_webgl()`, `print.nmr_dataset_1D()`, `rdCV_PLS_RF_ML()`, `rdCV_PLS_RF()`, `save_files_to_rDolphin()`, `to_ChemoSpec()`, `validate_nmr_dataset()`

Other peak detection functions: `Pipelines`, `nmr_baseline_threshold()`, `nmr_identify_regions_blood()`, `nmr_identify_regions_cell()`, `nmr_identify_regions_urine()`, `nmr_integrate_regions()`, `regions_from_peak_table()`

Other nmr_dataset_1D functions: `[.nmr_dataset_1D()`, `computes_peak_width_ppm()`, `file_lister()`, `files_to_rDolphin()`, `format.nmr_dataset_1D()`, `is.nmr_dataset_1D()`, `load_and_save_functions`, `new_nmr_dataset_1D()`, `nmr_align_find_ref()`, `nmr_baseline_removal()`, `nmr_baseline_threshold()`, `nmr_exclude_region()`, `nmr_integrate_regions()`, `nmr_interpolate_1D()`, `nmr_meta_add()`, `nmr_meta_export()`, `nmr_meta_get_column()`, `nmr_meta_get()`, `nmr_normalize()`, `nmr_pca_build_model()`, `nmr_pca_outliers_filter()`, `nmr_pca_outliers_plot()`, `nmr_pca_outliers_robust()`, `nmr_pca_outliers()`, `nmr_ppm_resolution()`, `plot.nmr_dataset_1D()`, `plot_webgl()`, `print.nmr_dataset_1D()`, `rdCV_PLS_RF_ML()`, `rdCV_PLS_RF()`, `save_files_to_rDolphin()`, `to_ChemoSpec()`, `validate_nmr_dataset()`

Other alignment functions: `Pipelines`, `nmr_align_find_ref()`

Other peak alignment functions: `nmr_align_find_ref()`

Other nmr_dataset_1D functions: `[.nmr_dataset_1D()`, `computes_peak_width_ppm()`, `file_lister()`, `files_to_rDolphin()`, `format.nmr_dataset_1D()`, `is.nmr_dataset_1D()`, `load_and_save_functions`, `new_nmr_dataset_1D()`, `nmr_align_find_ref()`, `nmr_baseline_removal()`, `nmr_baseline_threshold()`, `nmr_exclude_region()`, `nmr_integrate_regions()`, `nmr_interpolate_1D()`, `nmr_meta_add()`, `nmr_meta_export()`, `nmr_meta_get_column()`, `nmr_meta_get()`, `nmr_normalize()`, `nmr_pca_build_model()`, `nmr_pca_outliers_filter()`, `nmr_pca_outliers_plot()`, `nmr_pca_outliers_robust()`, `nmr_pca_outliers()`, `nmr_ppm_resolution()`, `plot.nmr_dataset_1D()`, `plot_webgl()`, `print.nmr_dataset_1D()`, `rdCV_PLS_RF_ML()`, `rdCV_PLS_RF()`, `save_files_to_rDolphin()`, `to_ChemoSpec()`, `validate_nmr_dataset()`

Other peak integration functions: `Pipelines`, `computes_peak_width_ppm()`, `nmr_identify_regions_blood()`, `nmr_identify_regions_cell()`, `nmr_identify_regions_urine()`, `nmr_integrate_regions()`

Other nmr_dataset_1D functions: `[.nmr_dataset_1D()`, `computes_peak_width_ppm()`, `file_lister()`, `files_to_rDolphin()`, `format.nmr_dataset_1D()`, `is.nmr_dataset_1D()`, `load_and_save_functions`, `new_nmr_dataset_1D()`, `nmr_align_find_ref()`, `nmr_baseline_removal()`, `nmr_baseline_threshold()`, `nmr_exclude_region()`, `nmr_integrate_regions()`, `nmr_interpolate_1D()`, `nmr_meta_add()`, `nmr_meta_export()`, `nmr_meta_get_column()`, `nmr_meta_get()`, `nmr_normalize()`, `nmr_pca_build_model()`, `nmr_pca_outliers_filter()`, `nmr_pca_outliers_plot()`, `nmr_pca_outliers_robust()`, `nmr_pca_outliers()`, `nmr_ppm_resolution()`, `plot.nmr_dataset_1D()`, `plot_webgl()`, `print.nmr_dataset_1D()`, `rdCV_PLS_RF_ML()`, `rdCV_PLS_RF()`, `save_files_to_rDolphin()`, `to_ChemoSpec()`, `validate_nmr_dataset()`

Other peak integration functions: `Pipelines`, `computes_peak_width_ppm()`, `nmr_identify_regions_blood()`, `nmr_identify_regions_cell()`, `nmr_identify_regions_urine()`, `nmr_integrate_regions()`

Other nmr_dataset_1D functions: `[.nmr_dataset_1D()`, `computes_peak_width_ppm()`, `file_lister()`, `files_to_rDolphin()`, `format.nmr_dataset_1D()`, `is.nmr_dataset_1D()`, `load_and_save_functions`, `new_nmr_dataset_1D()`, `nmr_align_find_ref()`, `nmr_baseline_removal()`, `nmr_baseline_threshold()`, `nmr_exclude_region()`, `nmr_integrate_regions()`, `nmr_interpolate_1D()`, `nmr_meta_add()`, `nmr_meta_export()`, `nmr_meta_get_column()`, `nmr_meta_get()`, `nmr_normalize()`, `nmr_pca_build_model()`, `nmr_pca_outliers_filter()`, `nmr_pca_outliers_plot()`, `nmr_pca_outliers_robust()`, `nmr_pca_outliers()`, `nmr_ppm_resolution()`, `plot.nmr_dataset_1D()`, `plot_webgl()`, `print.nmr_dataset_1D()`, `rdCV_PLS_RF_ML()`, `rdCV_PLS_RF()`, `save_files_to_rDolphin()`, `to_ChemoSpec()`, `validate_nmr_dataset()`

### Examples

    dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR")
    nmr_dataset <- nmr_read_samples_dir(dir_to_demo_dataset)
    dataset_1D <- nmr_interpolate_1D(nmr_dataset, axis = c(min = -0.5, max = 10, by = 2.3E-4))

    sample_10 <- filter(dataset_1D, NMRExperiment == "10")

    # 1.Peak detection in the dataset.
    peak_data <- nmr_detect_peaks(dataset_1D,
                                  nDivRange_ppm = 0.1, # Size of detection segments
                                  scales = seq(1, 16, 2),
                                  baselineThresh = 0, # Minimum peak intensity
                                  SNR.Th = 4) # Signal to noise ratio

    #nmr_detect_peaks_plot(sample_10, peak_data, "NMRExp_ref")

    peaks_detected <- nmr_detect_peaks_tune_snr(sample_10,
                                                SNR_thresholds = seq(from = 2,
                                                to = 3, by = 0.5))

    # 2.Find the reference spectrum to align with.
    NMRExp_ref <- nmr_align_find_ref(dataset_1D, peak_data)

    # 3.Spectra alignment using the ref spectrum and a maximum alignment shift
    nmr_dataset <- nmr_align(dataset_1D, # the dataset
                             peak_data, # detected peaks
                             NMRExp_ref = NMRExp_ref, # ref spectrum
                             maxShift_ppm = 0.0015, # max alignment shift
                             acceptLostPeak = FALSE) # lost peaks

    # 4.PEAK INTEGRATION (please, consider previous normalization step).
    # First we take the peak table from the reference spectrum
    peak_data_ref <- filter(peak_data, NMRExperiment == NMRExp_ref)

    # Then we integrate spectra considering the peaks from the ref spectrum
    nmr_peak_table <- nmr_integrate_peak_positions(
                          samples = nmr_dataset,
                          peak_pos_ppm = peak_data_ref$ppm,
                          peak_width_ppm = NULL)

    validate_nmr_dataset_peak_table(nmr_peak_table)

    #If you wanted the final peak table before machine learning you can run
    nmr_peak_table_completed <- get_integration_with_metadata(nmr_peak_table)

[Package AlpsNMR version 3.0.6 Index]