importSpectra: Import metabolomic spectra

In GaelleLefort/ASICS: Automatic Statistical Identification in Complex Spectra

Description

Import spectra from text or CSV, fid or 1r (preprocessed spectrum) files. (optional) Spectra are baseline corrected, aligned and normalised during the importation.

Usage

importSpectra(
  name.dir = NULL,
  name.file = NULL,
  type.import,
  baseline.correction = FALSE,
  alignment = FALSE,
  normalisation = TRUE,
  ncores = 1,
  verbose = TRUE,
  ...
)

Arguments

name.dir	Path of the folder containing the spectra. Each subfolder contains the fid or the 1r (preprocessed spectrum) files of this sample if type = "fid" or type = "1r".
name.file	Name of the txt or csv file containing the spectra in columns (spectrum names in the first line and ppm grid in the first column).
type.import	Type of import. Either "txt", "csv", "fid" or "1r".
baseline.correction	Logical. If TRUE a baseline correction is applied for each spectrum. Default to FALSE.
alignment	Logical. If TRUE a peak alignment is applied between all spectra. Default to FALSE.
normalisation	Logical. If TRUE a normalisation is applied for each spectrum (see normaliseSpectra for details). Default to TRUE.
ncores	Number of cores used in parallel evaluation. Default to 1.
verbose	A boolean value to allow print out process information.
...	Further arguments to be passed to the functions read.table, importSpectraBruker, Normalization (PepsNMR-package), alignSpectra or normaliseSpectra for specifying the parameters of the algorithm, if necessary.

Details

Some preprocessing steps are included during the importation. First, spectra are baseline corrected if baseline.correction = TRUE. Then, all spectrum definition domains are aligned to a unique one (either the one specified in ppm.grid or the grid of the default library). Finally, all spectra are normalised if normalisation = TRUE and aligned if alignment = TRUE.

Value

A data frame with spectra in columns and chemical shifts (in ppm) in rows.

References

Wang, K.C., Wang, S.Y., Kuo, C.H., Tseng Y.J. (2013). Distribution-based classification method for baseline correction of metabolomic 1D proton nuclear magnetic resonance spectra. Analytical Chemistry, 85(2), 1231-1239.

See Also

importSpectraBruker normaliseSpectra alignSpectra

Examples

## Import from txt file
current_path <- system.file("extdata", package = "ASICS")
spectra_data <- importSpectra(name.dir = current_path,
                     name.file = "spectra_example.txt", type.import = "txt")

## Import from fid file
current_path <- system.file("extdata", "example_spectra", package = "ASICS")
spectra_data <- importSpectra(name.dir = current_path, type.import = "fid",
                             subdirs = TRUE, dirs.names = TRUE)

## Import from txt file
current_path <- system.file("extdata", "example_spectra", package = "ASICS")
spectra_data <- importSpectra(name.dir = current_path, type.import = "1r")

GaelleLefort/ASICS documentation built on July 19, 2020, 2:08 p.m.