Warping: Warping of the spectra

Description Usage Arguments Details Value Author(s) References Examples

View source: R/Warping.R

Description

Warps the frequency x-axis to minimize the pairwise distance between a sample spectrum and a reference spectrum.

Usage

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Warping(Spectrum_data, normalization.type = c("median","mean",
        "firstquartile","peak","none"), fromto.normW = c(3.05, 4.05), 
        reference.choice = c("fixed", "before", 
        "after", "manual"), reference = 1, optim.crit = c("RMS", "WCC"), 
        ptw.wp = FALSE, K = 3, L = 40, lambda.smooth = 0, deg = 3, 
        lambda.bspline = 0.01, kappa = 0.0001, max_it_Bspline = 10, 
        returnReference = FALSE, returnWarpFunc = FALSE, verbose = FALSE)

Arguments

Spectrum_data

Matrix containing the spectra in ppm, one row per spectrum.

normalization.type

Type of normalization applied to the spectra prior to warping. See Normalization for details about the different types. none means that no normalization is applied. It is advised to use median instead of the default mean normalization.

fromto.normW

Used by Normalization when normalization.type is peak.

reference.choice

Specifies how the reference will be chosen:

"fixed"

The reference is specified by the rowname given in reference.

"before"

The reference is taken as the spectrum with the minimum sum of square difference with the other spectra.

"after"

Each spectrum is taken as the reference and the sum of square difference with the other spectra is calculated after the warping. See details below.

"manual"

The reference spectrum is specified in the reference argument.

reference

The row number or name of the reference spectrum when reference.choice is "fixed" or a numeric vector with the reference spectrum when reference.choice is "manual".

optim.crit

If ptw.wp is set to TRUE, WCC can also be considered as a criterion for optimization, see ptw::ptw for details.

ptw.wp

If set to TRUE, it applies the Parametric Time Warping with the ptw::ptw function to the data. In this case, the warping does not use B-splines and the arguments L, deg, lambda.bspline, kappa and max_it_Bspline are ignored.

K

It is the degree of the polynomial used for the warping (see details).

L

This is the number of B-splines that are used for the warping. It should be either 0 or greater than deg.

lambda.smooth

Nonnegative coefficient for the smoothing lambda.smooth = 0 means no smoothing. See ptw::difsm for more details.

deg

Degree of the B-splines.

lambda.bspline

Nonnegative second-order smoothness penalty coefficient for the B-splines warping. See the reference for more details.

kappa

Nonnegative ridge (zero-order) penalty coefficient for the B-splines warping. See the reference for more details.

max_it_Bspline

Maximum number of iterations for the B-splines warping.

returnReference

If TRUE, will return the name of the reference spectrum.

returnWarpFunc

If TRUE, will return the warping functions.

verbose

If "TRUE", will print processing information.

Details

When reference.choice is "after", the reference with the minimum sum is taken as the reference and the warped spectra according to this reference (that have already been calculated at this stage) are returned. This is n times slower than the 2 others where n is the number of spectra.

Principle:

We try to find a warping function between a reference spectrum and a sample. This function is a sum of polynomial of degree K and L B-splines of degree deg. The unknowns are the polynomial and B-splines coefficients.

No warping is equivalent to warping with a, the polynomial identity and all the coefficients of the B-splines with value 0. See the reference for details.

First, the polynomial is estimated on the reference and the sample both smoothed with parameter lambda.smooth. The B-splines are estimated on the non-smoothed reference and sample using the polynomial just found.

The higher lambda.bspline and kappa are, the less flexible the warping function will be.

Value

If returnReference = TRUE, the function will return the name of the reference spectrum and if returnWarpingfunc = TRUE, it will also return the warping functions.

Spectrum_data

The warped spectra.

Reference

The name of the reference spectrum.

Warpingfunc

The warping functions.

Author(s)

Benoît Legat, Manon Martin & Paul H. C. Eilers

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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require(PepsNMRData)
Warp.spec <- Warping(Data_HS_sp$Spectrum_data_HS_8, reference.choice="fixed", 
                             reference = row.names(Data_HS_sp$Spectrum_data_HS_8)[1],
                             returnReference = FALSE)
#or
Warp.res <- Warping(Data_HS_sp$Spectrum_data_HS_8, reference.choice="fixed", 
                             reference = row.names(Data_HS_sp$Spectrum_data_HS_8)[1],
                             returnReference = TRUE)
Warp.spec <- Warp.res[["Spectrum_data"]]
Warp.res[["Reference"]]

PepsNMR documentation built on Jan. 16, 2021, 2:07 a.m.