Convert to a Metabodecon Object — as_metabodecon

Convert a object to a Metabodecon object.

Usage

as_spectrum(x, sf = c(1000, 1e+06))

as_decon0(x, sf = NULL, spectrum = NULL, optional = TRUE)

as_decon1(
  x,
  sf = c(1000, 1e+06),
  spectrum = NULL,
  sfr = NULL,
  wshw = NULL,
  bwc = 2
)

as_decon2(
  x,
  sf = c(1000, 1e+06),
  spectrum = NULL,
  sfr = NULL,
  wshw = NULL,
  bwc = 2
)

as_spectra(
  x,
  file_format = "bruker",
  expno = 10,
  procno = 10,
  raw = FALSE,
  silent = TRUE,
  force = FALSE
)

as_decons0(x, sfs = list(c(1000, 1e+06)), spectra = list(NULL), nworkers = 1)

as_decons1(
  x,
  sfs = list(c(1000, 1e+06)),
  spectra = list(NULL),
  sfrs = list(NULL),
  wshws = list(NULL),
  bwc = 2,
  nworkers = 1
)

as_decons2(
  x,
  sfs = list(c(1000, 1e+06)),
  spectra = list(NULL),
  sfrs = list(NULL),
  wshws = list(NULL),
  bwc = 2,
  nworkers = 1
)

Arguments

x: The object to convert.
sf: Scale factor used during Only required if x is a decon0 object.
spectrum, spectra: The spectrum/spectra object corresponding to x as returned by read_spectrum() / read_spectra. Only required if x is a decon0 object.
optional: Logical. If TRUE, the two optional elements signal_free_region and range_water_signal_ppm are included in the returned decon0 object.
sfr, sfrs: sfr should be a vector specifying the borders of the signal free region. sfrs should be a list of such vectors. Only required if x is a decon0 object where element signal_free_region is missing (or a decons0 objected containing such decon0 objects).
wshw, wshws: wshw should specify the half width of the water signal region. wshws should be a list of such values. Only required if x is a decon0 object where element range_water_signal_ppm is missing (or a decons0 objected containing such decon0 objects).
bwc: Level of backwards compatibility. If bwc == 0, bug fixes introduced after version 0.2.2 of Metabodecon are not used. If bwc == 1, new features introduced after version 0.2.2 of Metabodecon (e.g. faster algorithms) are not used. If bwc == 2, all bug fixes and features introduced after version 0.2.2 are used. Support for bwc == 0 will be removed in 'metabodecon v2.0'.
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.
sfs: List of scale factors. Only required if x is a list of decon0 objects.
nworkers: Number of workers for parallel processing.

Value

An object of the specified class.

Author

2024-2025 Tobias Schmidt: initial version.

Examples

dirpath <- metabodecon_file("sim_subset")
spectra <- read_spectra(dirpath)
spectrum <- spectra[[1]]
decons1 <- generate_lorentz_curves_sim(spectra)
decon1 <- generate_lorentz_curves_sim(spectrum)
decon2 <- as_decon2(decon1)