Chemical Shift Calibration

Aligns 1D \(^1\)H NMR spectra to a reference signal on the existing ppm grid. Supports singlet (e.g. TSP or custom range) and predefined doublet references (glucose, alanine).

Usage

calibrate(X, ppm = NULL, type = "tsp")

Arguments

X

Numeric matrix/vector of spectra or a metabom8 data list.

ppm

Numeric chemical shift vector. If X is a metabom8 list, this is taken from X$ppm.

type

Character ("tsp", "glucose", "alanine"), or list.

Value

Calibrated spectra in the same structure as input.

Details

In addition to predefined references, custom calibration targets can be supplied as a list with elements:

• mode: "singlet" or "doublet"

• window: numeric vector of length 2 defining the ppm search region

• centre: target ppm position (optional; defaults to mean(window))

• j: numeric vector of length 2 specifying expected J-coupling (required for doublet calibration)

Custom doublet calibration requires the expected J-coupling range (j) in ppm to distinguish the two peaks of the multiplet.

For example:

calibrate(
  X, ppm,
  list(
    mode   = "doublet",
    window = c(1.2, 1.35),
    j      = c(0.007, 0.009)
  )
)

See also

Other preprocessing: align_segment(), align_spectra(), binning(), correct_baseline(), correct_lw(), pqn(), print_preprocessing()

Examples

data("covid_raw")
X=covid_raw$X
ppm=covid_raw$ppm
X_tsp <- calibrate(X, ppm, type = "tsp")
X_glu <- calibrate(X, ppm, type = "glucose")
X_custom <- calibrate(X, ppm, type = c(1.9, 2.1))