ZeroOrderPhaseCorrection: Zero Order Phase Correction
In yclement/PepsNMR: Pre-process 1H-NMR FID signals

Description Usage Arguments Details Value Author(s) References Examples

View source: R/ZeroOrderPhaseCorrection.R

The function corrects the spectra in order to have their real part in an absorptive mode.

ZeroOrderPhaseCorrection(Spectrum_data, type.zopc = c("rms", "manual", "max"), 
                        plot_rms = NULL, returnAngle = FALSE, 
                        createWindow = TRUE, angle = NULL, plot_spectra = FALSE,  
                        ppm.zopc = TRUE, exclude.zopc = list(c(5.1,4.5)), verbose = FALSE)

`Spectrum_data`	Matrix containing the spectra in ppm, one row per spectrum.
`type.zopc`	Method used to select the angles to rotate the spectra. See details.
`plot_rms`	Contains a vector of row names for which a debug plot should be made showing the value of the function we try to minimize as a function of the phase.
`returnAngle`	If `TRUE`, will return the rotation angle used for phase correction.
`createWindow`	If `TRUE`, will open a new window to draw the rms or spectra plots, if `FALSE`, plots are drawn in the current device.
`angle`	If not `NULL`, a numeric vector with angles specified in radian to manually rotate the spectra, one angle per spectrum. By convention, the spectra are rotated with the correction angle `- angle`.
`plot_spectra`	If `TRUE`, will draw real and imaginary parts of the rotated spectra.
`ppm.zopc`	If `TRUE`, the values in `exclude.zopc` represent frequencies in ppm value (column names of spectra), if `FALSE` these values are column indices.
`exclude.zopc`	If not `NULL`, a list containing the extremities of the intervals excluded for the computation of the positiveness criterion, either expressed in ppm (decreasing values) OR in column indices (increasing values), e.g. `exclude.zopc = list(c(0,10000))` if `ppm.zopc == FALSE` or `exclude.zopc = list(c(1,-1))` if `ppm.zopc == TRUE`.
`verbose`	If `"TRUE"`, will print processing information.

We focus our optimization on the positiveness of the real part which should be in an absoptive mode.

When type.zopc is "rms", a positiveness criterion is measured for each spectrum. "manual" is used when a vector of angles are specified in angle and "max" will optimize the maximum spectral intensity in the non-excluded window(s). Beware that if exclude.zopc is not NULL, the optimization will only consider the non-excluded spectral window(s).

By default the water region (5.1 - 4.5) is ignored.

BaselineCorrection and NegativeValuesZeroing will take care of the last negative values of the real part of the spectra. See the reference for more details.

Spectrum_data

The matrix of rotated spectra.

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).

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require(PepsNMRData)
Zopc.res <- ZeroOrderPhaseCorrection(Data_HS_sp$Spectrum_data_HS_4, 
            ppm.zopc = FALSE, exclude.zopc = list(c(5000,15000)))