Create a Spectrum Object

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.

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)
#> 2025-01-20 11:57:49.82 Calculated spectrum width in Hz (12005) does not match the provided value (12010). Continuing anyways, because `force` equals `TRUE`. Please note that all downstream calculations using frequencies might be wrong, so be sure to double check the results.