PreprocessingChain: Proprocessing workflow for 1H-NMR data

Description Usage Arguments Value Author(s) References Examples

View source: R/PreprocessingChain.R

Description

The function is a wrapper for all the preprocessing steps available in PepsNMR.

Usage

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PreprocessingChain(Fid_data = NULL, Fid_info = NULL, data.path = NULL, readFids = TRUE, 
    groupDelayCorr = TRUE, solventSuppression = TRUE, apodization = TRUE, 
    zerofilling = TRUE,fourierTransform = TRUE, zeroOrderPhaseCorr = TRUE, 
    internalReferencing = TRUE, baselineCorrection = TRUE, negativeValues0 = TRUE, 
    warping = TRUE, windowSelection = TRUE, bucketing = TRUE, regionRemoval = TRUE, 
    zoneAggregation = TRUE,normalization = TRUE, ...,  export = FALSE, 
    format = c("Rdata", "csv", "txt"), out.path = ".",  filename = "filename", 
    writeArg = c("none", "return", "txt"), verbose = FALSE)

Arguments

Fid_data

If non NULL, matrix containing the complex FIDs, one row per FID.

Fid_info

If non NULL, matrix containing the information for each spectrum, one row per spectrum, as returned by ReadFids.

data.path

A character string specifying the directory where the FIDs are searched.

readFids

If TRUE, applies the ReadFids function to the data.

groupDelayCorr

If TRUE, applies the GroupDelayCorrection function to the data.

solventSuppression

If TRUE, applies the SolventSuppression function to the data.

apodization

If TRUE, applies the Apodization function to the data.

zerofilling

If TRUE, applies the ZeroFilling function to the data.

fourierTransform

If TRUE, applies the FourierTransform function to the data.

zeroOrderPhaseCorr

If TRUE, applies the ZeroOrderPhaseCorrection function to the data.

internalReferencing

If TRUE, applies the InternalReferencing function to the data.

baselineCorrection

If TRUE, applies the BaselineCorrection function to the data.

negativeValues0

If TRUE, applies the NegativeValuesZeroing function to the data.

warping

If TRUE, applies the Warping function to the data.

windowSelection

If TRUE, applies the WindowSelection function to the data.

bucketing

If TRUE, applies the Bucketing function to the data.

regionRemoval

If TRUE, applies the RegionRemoval function to the data.

zoneAggregation

If TRUE, applies the ZoneAggregation function to the data.

normalization

If TRUE, applies the Normalization function to the data.

...

Other optionnal arguments of the above pre-processing functions.

export

If TRUE, will export the spectral intensities and the aquisition parameters matrices.

format

Format chosen to export the spectral intensities and the aquisition parameters matrices.

out.path

Path used to export the spectral intensities and the aquisition parameters matrices if export == TRUE and the function argument if writeArg == "txt".

filename

Name given to exported files.

writeArg

If not "none", will export the function arguments, either in the return of the function ("return") or as a text file ("txt").

verbose

If "TRUE", will print processing information.

Value

The function will return a list with the spectral intensities and the aquisition parameters matrices. If writeArg == "return", an additionnal list element is returned (arguments).

Spectrum_data

The pre-processed spectra.

Fid_info

The acquisition parameters.

arguments

The function arguments.

Author(s)

Manon Martin

References

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).

Examples

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path <-  system.file("extdata", package = "PepsNMRData")
data.path <-  file.path(path, "HumanSerum")
res <-  PreprocessingChain(Fid_data = NULL, Fid_info = NULL, data.path = data.path, 
      ReadFids = TRUE, type.norm = "mean", export = FALSE, writeArg = "return")

ManonMartin/PepsNMR documentation built on Nov. 28, 2021, 6:22 p.m.