metabodecon (version 1.6.2)

as_metabodecon_class: Convert to a Metabodecon Object

Description

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
)

Value

An object of the specified class.

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.

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)