cali: Chemical Shift Calibration

In kylebario/concentr8r: MRS Data Preprocessing and Normalisation

Chemical Shift Calibration

Description

Chemical shift calibration with a reference signal.

Usage

cali(X, ppm, type = c("tsp"))

Arguments

X	num matrix, NMR data matrix with rows representing spectra and columns representing chemical shift position
ppm	num vector, matched to columns of X
type	str or num. Str: Either 'tsp' or 'glucose' for urine or blood-derived spectra, respectively (see Details). Num: ppm range of max height signal that will be used to reference to zero

Details

Spectral calibration to a selected chemical shift reference signal. type='tsp': calibration to 0 ppm using the highest peak located in interval 0 +/- 0.20 ppm (Trimethylsilylpropanoic acid resonance)

Value

num matrix X, calibrated NMR data matrix.

Author(s)

[e-mail]

References

Dona, A.C., et al. (2014) Precision high-throughput proton NMR spectroscopy of human urine, serum, and plasma for large-scale metabolic phenotyping. Analytical Chemistry. 86.19. 9887-94.

See Also

Other preproc: bl(), preproc(), read_in()

Examples

read_in(path = system.file('extdata',package='concentr8r'),
        exp_type = list(exp=c("PROF_URINE_NOESY")),
        n_spec = 'multiple')
plot(ppm, X[2,], type = 'l', col = 'red',
    main = 'NMR Spectra (Processed vs. Non Processed)',
    xlab = 'Chemical Shift (ppm)', ylab = 'Intensity', xlim = c(10,-1))
Xc=cali(X, ppm, type='tsp')
points(ppm, X[2,], type = 'l', col = 'blue')
legend('topleft', legend = c("Uncalibrated", "Calibrated"), col = c('red', 'blue'), lty = 1)

kylebario/concentr8r documentation built on Nov. 9, 2022, 12:47 a.m.