PEPSNMR-package: Metabolomic data pre-processing strategy for 1H NMR...
In yclement/PepsNMR: Pre-process 1H-NMR FID signals

Description Details Author(s) References Examples

This package provides R functions for classic and advanced pre-processing steps that are applied on 1H NMR data. It also provides the function ReadFids to read the FID directly from the Bruker format. Those pre-processing are cited below in the advised order of their application:

GroupDelayCorrection: Correct for the first order phase correction.
SolventSuppression: Remove solvent signal from the FIDs.
Apodization: Increase the sensitivity/resolution of the FIDs.
ZeroFilling: Improve the visual representation of the spectra.
FourierTransform: Transform the FID into a spectrum and convert the frequency scale (Hertz -> ppm).
ZeroOrderPhaseCorrection: Correct for the zero order phase correction.
InternalReferencing: Calibrate the spectra with internal compound referencing.
BaselineCorrection: Remove the spectral baseline.
NegativeValuesZeroing: Set negatives values to 0.
Warping: Warp the samples according to a reference spectrum.
WindowSelection: Select the informative part of the spectrum.
Bucketing: Data reduction by integration.
RegionRemoval: Set intensities of a desired region to 0.
ZoneAggregation: Aggregate a region to a single peak.
Normalization: Normalize the spectra.

Package:	PepsNMR
Type:	Package
Version:	0.99.0
License:	GPLv2

The FIDs are read using ReadFids which also gives a matrix with meta-information about each FID. The other functions apply different pre-processing steps on these signals, and some need the info matrix as outputted from ReadFids . During this pre-processing, the signal is transformed through fourier transformation and the frequency scale is expressed in ppm. For more details and illustrated explanations about those pre-treatment steps, see the documentation of each function and/or the chapter 1 of the reference below.

Benoît Legat, Bernadette Govaerts & Manon Martin

Maintainer: Manon Martin <manon.martin@uclouvain.be>

Martin, M., Legat, B., Leenders, J., Vanwinsberghe, J., Rousseau, R., Boulanger, B., & Govaerts, B. (2018). PepsNMR for 1H NMR metabolomic data pre-processing. Analytica chimica acta, 1019, 1-13.

Rousseau, R. (2011). Statistical contribution to the analysis of metabonomics data in 1H NMR spectroscopy (Doctoral dissertation, PhD thesis. Institut de statistique, biostatistique et sciences actuarielles, Université catholique de Louvain, Belgium).

path <-  system.file("extdata", package = "PepsNMRData")
dir(path)

fidList <- ReadFids(file.path(path, "HumanSerum"))
Fid_data <- fidList[["Fid_data"]]
Fid_info <- fidList[["Fid_info"]]
Fid_data <- GroupDelayCorrection(Fid_data, Fid_info)
Fid_data <- SolventSuppression(Fid_data)
Fid_data <- Apodization(Fid_data, Fid_info)
Fid_data <- ZeroFilling(Fid_data)
Spectrum_data <- FourierTransform(Fid_data, Fid_info)
Spectrum_data <- ZeroOrderPhaseCorrection(Spectrum_data)
Spectrum_data <- InternalReferencing(Spectrum_data, Fid_info)
Spectrum_data <- BaselineCorrection(Spectrum_data)
Spectrum_data <- NegativeValuesZeroing(Spectrum_data)
Spectrum_data <- Warping(Spectrum_data)
Spectrum_data <- WindowSelection(Spectrum_data)
Spectrum_data <- Bucketing(Spectrum_data)
Spectrum_data <- RegionRemoval(Spectrum_data, typeofspectra = "serum")
# Spectrum_data <- ZoneAggregation(Spectrum_data)
Spectrum_data <- Normalization(Spectrum_data, type.norm = "mean")