make_spectrum: Create a Spectrum Object

In metabodecon: Deconvolution and Alignment of 1d NMR Spectra

Create a Spectrum Object

Description

Creates a spectrum object from the provided signal intensities, frequencies and chemical shifts.

Usage

make_spectrum(
  si,
  cs_max,
  cs_width,
  fq_ref,
  fq_width = NULL,
  force = FALSE,
  silent = FALSE,
  name = NULL,
  path = NULL,
  type = NULL,
  simpar = NULL,
  mfs = NULL
)

Arguments

si	Numeric vector of signal intensities, ordered from highest to lowest corresponding chemical shift.
cs_max	The highest chemical shift value in ppm, usually shown as left end of the spectrum.
cs_width	The width of the spectrum in ppm.
fq_ref	The reference frequency in Hz.
fq_width	The width of the spectrum in Hz. Only used to check whether the values calculated from cs_max, cs_width and fq_ref match the provided value. If NULL, this check will be skipped.
force	If TRUE, the function will not raise an error in case of discrepancies between the calculated and the provided spectrum width in Hz, but will print a info message instead. To hide this message as well, set silent = TRUE.
silent	If TRUE, no output will be printed to the console.
name	The name of the spectrum, e.g. "Blood 1" or "Urine Mouse X23D".
path	The path to the spectrum file, e.g. "/example_datasets/bruker/urine/urine_1".
type	The type of experiment, e.g. "H1 CPMG" or "H1 NOESY".
simpar	The simulation parameters used to generate the spectrum.
mfs	The magnetic field strength in Tesla.

Value

A spectrum object as described in Metabodecon Classes.

Author(s)

2024-2025 Tobias Schmidt: initial version.

Examples

si <- c(1, 1, 3, 7, 8, 3, 8, 5, 2, 1)
cs_max <- 14.8
cs_width <- 20.0
fq_ref <- 600.25 * 1e6
fq_width <- 12005
spectrum <- make_spectrum(si, cs_max, cs_width, fq_ref, fq_width)
spectrum2 <- make_spectrum(si, cs_max, cs_width, fq_ref, fq_width = 12010, force = FALSE)

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