RegionRemoval: Removal of non-informative regions
In yclement/PepsNMR: Pre-process 1H-NMR FID signals

Description Usage Arguments Details Value Author(s) References Examples

Removes the non-informative regions by setting the values of the spectra in these intervals to zero.

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RegionRemoval(Spectrum_data, typeofspectra = c("manual", "serum", "urine"), 
                          type.rr = c( "zero", "NA"), 
                          fromto.rr = list(Water = c(4.5, 5.1)), verbose = FALSE)

`Spectrum_data`	Matrix containing the spectra in ppm, one row per spectrum.
`typeofspectra`	Type of spectra, if not `"manual"`, will automatically remove unwanted regions depending on the nature of spectra.
`type.rr`	Type of region removal method. If `type.rr = "zero"`, intensities are set to 0; if `type.rr = "NA"`, intensities are set to NA.
`fromto.rr`	List containing the extremities of the intervals to be removed.
`verbose`	If `"TRUE"`, will print processing information.

The presence of non-informative regions can strongly bias the subsequent statistical analysis.

The inclusive ppm interval fromto.rr is set to zero or completed with NAs for every spectrum. The ppm scale can be increasing or decreasing (i.e. from < to or from > to).

The type of spectra can be NULL to manually specify the area to be removed otherwise it is specified as typeofspectra = "serum" or typeofspectra = "urine" and the removed area are for typeofspectra = "serum": water (4.5 - 5.1 ppm) and for typeofspectra = "urine": water, uree and maleic acid (4.5 - 6.1 ppm).

Spectrum_data

The matrix of spectra with the removed regions.

Benoît Legat & Manon Martin

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).

# Remove the lactate and water regions for serum spectra
require(PepsNMRData)
fromto <- list(Water =c(4.5, 5.1), Lactate=c(1.32, 1.36))
Rr.spec <- RegionRemoval(Data_HS_sp$Spectrum_data_HS_11,fromto.rr = fromto)