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Read Raw 1D NMR FIDs and Process to Spectra

Source: R/read1d_raw.R
read1d_raw.Rd

Reads Bruker 1D NMR FIDs from directories, applies apodisation and FFT, phases and calibrates the spectrum, and returns absorption, dispersion, or magnitude mode spectra. Results are assigned to the global environment.

Usage

read1d_raw(
  path,
  exp_type = list(exp = "PROF_PLASMA_CPMG128_3mm", pulprog = "noesygppr1d"),
  apodisation = list(fun = "exponential", lb = 0.2),
  zerofil = 1L,
  return = "absorption",
  verbose = 1,
  recursive = TRUE,
  n_max = 1000,
  filter = TRUE
)

Arguments

path

Character. Path to the root directory containing Bruker experiment folders.

exp_type

Named list. Filter for acquisition parameters to select experiments (e.g., list(exp = "noesygppr1d")).

apodisation

Named list. Specifies apodisation function and parameters. fun must be one of: "exponential", "cosine", "sine", "sem".

zerofil

Integer. Zerofilling exponent (e.g., 1 doubles points, 2 quadruples).

return

Character. Spectrum type to return: "absorption", "dispersion", or "magnitude".

verbose

Integer. Verbosity level: 0 = silent, 1 = summary (default), 2 = detailed, 3 = debug mode.

recursive

Logical. Whether to recursively search subdirectories for FIDs.

n_max

Integer. Maximum number of experiments to process.

filter

Logical. Whether to remove experiments with incomplete file structures.

Value

The function assigns three objects into the global environment:

X

Numeric matrix of spectra (rows = samples, columns = ppm values).

ppm

Numeric vector of chemical shift axis (ppm).

meta

Data.frame with spectrometer parameters, row-matched to X.

Existing objects named X, ppm, or meta will be overwritten.

Details

Reads FID data from Bruker acquisition folders and applies digital signal processing: apodisation, zerofilling, FFT, phase correction, and calibration to TSP. A common ppm scale is interpolated across spectra.

Apodisation functions:

  • "exponential" (requires lb)

  • "cosine", "sine", "sem"

See also

read1d for TopSpin-processed spectra

Other NMR: alignSegment(), binning(), cvanova(), get_idx(), lw(), matspec(), noise.est(), normErectic(), read1d(), stocsy1d_metabom8-class, storm()

Examples

path <- system.file("extdata", package = "metabom8")
read1d_raw(path, exp_type = list(pulprog = "noesygppr1d"),
           apodisation = list(fun = "exponential", lb = 0.2), n_max = 3)
#> Reading 1 experiments.
#> Assigning objects X, ppm, meta to global environment.