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Peak detection for NMR

Source: R/nmr_detect_peaks_align.R
nmr_detect_peaks.Rd

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.

Usage

nmr_detect_peaks(
  nmr_dataset,
  nDivRange_ppm = 0.1,
  scales = seq(1, 16, 2),
  baselineThresh = NULL,
  SNR.Th = 3,
  range_without_peaks = c(9.5, 10),
  fit_lorentzians = FALSE,
  verbose = FALSE
)

Arguments

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

All peaks with intensities below the thresholds are excluded. Either:

  • A numeric vector of length the number of samples. Each number is a threshold for that sample

  • A single number. All samples use this number as baseline threshold.

  • NULL. If that's the case, a default function is used (nmr_baseline_threshold()), which assumes that there is no signal in the region 9.5-10 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.

range_without_peaks

A numeric vector of length two with a region without peaks, only used when baselineThresh = NULL

fit_lorentzians

If TRUE, fit a lorentzian to each detected peak, to infer its inflection points. For now disabled for backwards compatibility.

verbose

Logical (TRUE or FALSE). Show informational messages, such as the estimated baseline

Value

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

Details

Optionally afterwards, the peak apex and the peak inflection points are used to efficiently adjust a lorentzian to each peak, and compute the peak area and width, as well as the error of the fit. These peak features can be used afterwards to reject false detections.

See also

nmr_align for peak alignment with the detected peak table

Peak_detection

Other peak detection functions: Pipelines, nmr_baseline_threshold(), nmr_detect_peaks_plot(), nmr_detect_peaks_plot_overview(), nmr_detect_peaks_tune_snr(), nmr_identify_regions_blood(), nmr_identify_regions_cell(), nmr_identify_regions_urine(), nmr_integrate_regions()