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Metabodecon Classes

Source: vignettes/Classes.Rmd
Classes.Rmd

Metabodecon introduces a set of classes to highlight the presence of certain elements in corresponding objects. The order of elements may vary between different versions of Metabodecon, thus elements should always be accessed by name, for example, using x$si or x[["cs"]].

The classes itself are described in section Class Overview. The elements associated with a class are described in section Elements. A graphical visualization of the classes and their corresponding functions is given in figure Metabodecon Workflow.

Class Overview

spectrum

Represents one NMR spectrum. Objects of class ‘spectrum’ have at least elements 1-3 from section Elements v1.2+.

decon0

Represents one deconvoluted NMR spectrum stored in the old MetaboDecon1D() format. Objects of class ‘decon0’ have at least elements 1-18 from section Elements v0.2+.

decon1

Represents one deconvoluted NMR spectrum stored in the backwards compatible generate_lorentz_curves() format. Objects of class ‘decon1’ have all elements from section Elements v0.2+.

decon2

Represents one deconvoluted NMR spectrum stored in the new deconvolute() format. Objects of class ‘decon2’ have all elements from section Elements v1.2+ with elements sit$al and lcpar$x0al set to NULL.

align

Represents one deconvoluted NMR spectrum for which the individual peaks have been aligned using [align()]. Objects of class ‘align’ have all elements from section Elements v1.2+.

Collections

The classes mentioned above represent individual objects, such as a single spectrum, deconvolution, or alignment. However, it is often useful to describe collections of these objects, such as a list of spectra or deconvolutions. Therefore, for each individual class, a corresponding “collection” class is provided. These collection classes are named: spectra, decons0, decons1, decons2, and aligns.

Elements

Elements v1.2+

  1. cs: Vector of chemical shifts (CS) in parts per pillion (ppm). Must be of the same length as si.
  2. si: Vector of signal intensities (SI) in arbitrary units (au). Element si[i] is the signal intensity measured at chemical shift cs[i], i.e. si must be of the same length as cs.
  3. meta: List of additional metadata about the spectrum, e.g.:
    • name: The name of the spectrum, e.g. "Blood 1" or "Urine 2".
    • path: The path of the file/folder containing the spectrum data. E.g. "example_datasets/jcampdx/urine/urine_1.dx" or "example_datasets/bruker/urine/urine".
    • type: The type of experiment, e.g. "H1 CPMG" or "H1 NOESY".
    • fq: Vector of signal frequencies in Hertz (Hz). Must be of the same length as si and cs.
    • mfs: Magnetic field strength in Tesla, e.g. 14.1.
    • simpar: True Lorentz Curve parameters. List with elements A, lambda and x0. For details see element lcpar. Only available if a spectrum has been simulated.
  4. args: List of deconvolution parameters:
    • nfit: The number of fitting iterations.
    • smopts: The smoothing parameters used for the deconvolution.
    • delta: The threshold used for peak filtering.
    • sfr: Borders of the signal free region in ppm.
    • wshw: Water signal half width in ppm.
  5. sit: Dataframe of Signal Intensities (SI) after applying various transformations:
    • wsrm: SIs after Water Signal Removal (WSRM),
    • nvrm: SIs after WSRM and Negative Value Removal (NVRM).
    • sm: SIs after WSRM, NVRM and smoothing.
    • sup: SIs as superposition of Lorentz Curves.
    • al: SIs after alignment.
  6. peak: Dataframe of peak triplets found during peak selection:
    • center: Indices of peak centers.
    • left: Indices of left borders.
    • right: Indices of right peak borders.
  7. lcpar: Dataframe of Lorentz Curve parameters after parameter approximation:
    • A: Amplitude parameter.
    • lambda: Halfwidth parameter.
    • x0: Center parameter.
    • x0al: Center parameter after the spectrum has been aligned.
  8. mse: List of Mean squared error (MSE):
    • raw: MSE between si and sit$sup
    • norm: MSE between si and sit$sup, divided by sum(sit$sup)
    • sm: MSE between sit$sm and sit$sup
    • smnorm: MSE between sit$sm and sit$sup, divided by sum(sit$sup). Equals mse_normed in Elements v0.2+.

Elements v0.2+

  1. filename: Name of the analyzed spectrum.
  2. x_values: Scaled datapoint numbers (SDP). Datapoints are numbered in descending order going from N-1 to 0, where N equals the total amount of data points. Scaled data point numbers are obtained by dividing these numbers by the scale factor of the x-axis. I.e., for a spectrum with 131072 datapoints and a scale factor of 1000, the first scale datapoint has value 131.071 and the last one has value 0.
  3. x_values_ppm: The chemical shift of each datapoint in ppm (parts per million).
  4. y_values: The scaled signal intensity (SSI) of each datapoint. Obtained by reading the raw intensity values from the provided data_path as integers and dividing them scale factor of the y-axis.
  5. spectrum_superposition: Scaled signal intensity obtained by calculating the sum of all estimated Lorentz Curves for each data point.
  6. mse_normed: where is the normalized, smoothed signal intensity of data point i and is the normalized superposition of Lorentz Curves at data point i. Normalized in this context means that the vectors were scaled so the sum over all data points equals 1.
  7. peak_triplets_middle: Chemical shift of peak centers in ppm.
  8. peak_triplets_left: Chemical shift of left peak borders in ppm.
  9. peak_triplets_right: Chemical shift of right peak borders in ppm.
  10. index_peak_triplets_middle: Datapoint numbers of peak centers.
  11. index_peak_triplets_left: Datapoint numbers of left peak borders.
  12. index_peak_triplets_right: Datapoint numbers of right peak borders.
  13. integrals: Integrals of the Lorentz Curves.
  14. signal_free_region: Borders of the signal free region of the spectrum in scaled datapoint numbers. Left of the first element and right of the second element no signals are expected. Only available if MetaboDecon1D() was called with more than one spectra as input.
  15. range_water_signal_ppm: Half width of the water signal in ppm. Potential signals in this region are ignored. Only available if MetaboDecon1D() was called with more than one spectra as input.
  16. A: Amplitude parameter of the Lorentz Curves. Provided as negative number to maintain backwards compatibility with MetaboDecon1D. The area under the Lorentz Curve is calculated as .
  17. lambda: Half width of the Lorentz Curves in scaled data points. Provided as negative value to maintain backwards compatibility with MetaboDecon1D. Example: a value of -0.00525 corresponds to 5.25 data points. With a spectral width of 12019 Hz and 131072 data points this corresponds to a halfwidth at half height of approx. 0.48 Hz. The corresponding calculation is: (12019 Hz / 131071 dp) * 5.25 dp.
  18. x_0: Center of the Lorentz Curves in scaled data points.
  19. y_values_raw: The raw signal intensity of each datapoint
  20. x_values_hz: The frequency of each datapoint in Hz
  21. mse_normed_raw: Normalized mean squared error when comparing the raw signal intensities with the superposition of Lorentz Curves.
  22. x_0_hz: Center of the Lorentz Curves in Hz.
  23. x_0_dp: Center of the Lorentz Curves in data points.
  24. x_0_ppm: Center of the Lorentz Curves in ppm.
  25. A_hz: Amplitude parameter of the Lorentz Curves in Hz.
  26. A_dp: Amplitude parameter of the Lorentz Curves in data points.
  27. A_ppm: Amplitude parameter of the Lorentz Curves in ppm.
  28. lambda_hz: Half width of the Lorentz Curves in Hz.
  29. lambda_dp: Half width of the Lorentz Curves in data points.
  30. lambda_ppm: Half width of the Lorentz Curves in ppm.

Metabodecon Workflow

Metabodecon Workflow
Metabodecon Workflow