detectSpecPeaks: Peak detection for spectra

In speaq: Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and Visualizations

Peak detection for spectra

Description

Divide the whole spectra into smaller segments and detect peaks by using MassSpecWavelet package. Note that, the peak lists could be found by using other methods, this function is just a choice.

Usage

detectSpecPeaks(
  X,
  nDivRange = 128,
  scales = seq(1, 16, 2),
  baselineThresh = 50000,
  SNR.Th = -1,
  verbose = TRUE
)

Arguments

X	The spectral dataset in matrix format in which each row contains a single sample
nDivRange	The size of a single small segment after division of spectra
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.
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.
verbose	A boolean value to allow print out process information.

Value

The peak lists of the spectra

Author(s)

Trung Nghia Vu

Examples

res=makeSimulatedData();
X=res$data;
groupLabel=res$label;
peakList <- detectSpecPeaks(X,
                            nDivRange = c(128),
                            scales = seq(1, 16, 2),
                            baselineThresh = 50000,
                            SNR.Th = -1,
                            verbose=FALSE
);

speaq documentation built on May 23, 2022, 5:06 p.m.