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Import 1D NMR spectra (TopSpin processed)

Source: R/io_read1d.R
read1d.Rd

Imports TopSpin-processed 1D NMR spectra together with spectrometer acquisition and TopSpin processing parameters (acqus and procs, respectively).

Usage

read1d(
  path,
  exp_type = list(pulprog = "noesygppr1d"),
  n_max = 1000,
  filter = TRUE,
  recursive = TRUE,
  verbose = 1,
  to_global = FALSE
)

read1d_proc(
  path,
  exp_type = list(pulprog = "noesygppr1d"),
  n_max = 1000,
  filter = TRUE,
  recursive = TRUE,
  verbose = 1,
  to_global = FALSE
)

Arguments

path

Character. Directory path containing Bruker NMR experiments.

exp_type

Named list. Optional filtering specification based on acquisition or processing metadata. Each list element must correspond to a metadata field (e.g. pulprog, ns, rg). Filtering supports:

  • Exact match: list(pulprog = "noesygppr1d")

  • Membership: list(pulprog = c("zg30", "noesygppr1d"))

  • Numeric range: list(ns = list(range = c(16, 128)))

  • Generic comparison: list(ns = list(op = ">=", value = 32))

Multiple fields are combined using logical AND.

n_max

Integer. Maximum number of spectra to import. Default: 1000.

filter

Logical. Filter out experiments with incomplete file systems.

recursive

Logical. Search path recursively. Default: TRUE.

verbose

Logical or numeric. Verbosity level.

to_global

Logical. If TRUE, the returned objects are additionally assigned to the global environment.

Value

A named list with three elements:

X

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

ppm

A numeric vector of chemical shift values (ppm).

meta

A data frame of acquisition and processing metadata, row-aligned with X.

If to_global = TRUE, objects with the same names in the global environment will be overwritten.

Examples

path <- system.file("extdata", package = "metabom8")

read1d_proc(path, exp_type = list(pulprog = "noesygppr1d"), n_max = 2)
#> Imported 2 spectra.