read_spectra: Read one or more spectra from Disk

In metabodecon: Deconvolution and Alignment of 1d NMR Spectra

Read one or more spectra from Disk

Description

read_spectrum() reads a single spectrum from disk and returns it as spectrum object. read_spectra() can be used to read multiple spectra at once and returns a spectra object.

Usage

read_spectra(
  data_path = pkg_file("example_datasets/bruker/urine"),
  file_format = "bruker",
  expno = 10,
  procno = 10,
  raw = FALSE,
  silent = TRUE,
  force = FALSE
)

Arguments

data_path	The path of the file/folder containing the spectrum data. E.g. "example_datasets/jcampdx/urine/urine_1.dx" or "example_datasets/bruker/urine/urine".
file_format	The file_format of the spectrum file. E.g. "bruker" or "jcampdx".
expno, procno	The experiment/processing number for the file. E.g. "10". Only relevant if file_format equals "bruker". For details see section File Structure in the metabodecon FAQ.
raw	If FALSE, scales the returned signal intensities based on information available in the spectrum metadata, in particular NC_proc. For details see processing-reference.pdf, available at https://www.bruker.com/en.html at section 'Services & Support > Documentation & Manuals > Magnetic Resonance > Acquisition & Processing > TopSpin Processing Commands and Parameters' (requires login).
silent	If TRUE, no output will be printed to the console.
force	If TRUE, try to continue when encountering errors and print info messages instead. To hide these messages as well, set silent = TRUE.

Value

A spectrum object as described in Metabodecon Classes.

Author(s)

2024-2025 Tobias Schmidt: initial version.

Examples

relpath <- "example_datasets/bruker/urine"
urine <- system.file(relpath, package = "metabodecon")
urine_1 <- file.path(urine, "urine_1")
urine_2 <- file.path(urine, "urine_2")
x1 <- read_spectrum(urine_1)
x2 <- read_spectrum(urine_2)
xx <- read_spectra(urine)
str(xx)
str(x1)
stopifnot(all.equal(x1, xx$urine_1))

metabodecon documentation built on Nov. 5, 2025, 7:12 p.m.