PepsNMR-package {PepsNMR} | R Documentation |
This package provides R functions for classic and advanced preprocessing steps that are applied
on 1H NMR data.
It also provides the function ReadFids
to read the FID directly from the Bruker format.
Those preprocessing 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 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 preprocessing steps on these signals, and some need the info matrix as outputted from ReadFids
.
During this preprocessing, 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")