importSpectraBruker {ASICS}R Documentation

Import metabolomic spectra from Bruker files

Description

Import spectra from Bruker files contained in a single folder. This folder contains one subfolder for each sample. Spectra are baseline corrected (optional) and normalised by the area under the curve during the importation.

Usage

importSpectraBruker(name.dir, which.spectra = "last",
  baseline.correction = TRUE, alignment = FALSE, ppm.grid = NULL,
  sample.names = NULL, ncores = 1, ...)

Arguments

name.dir

Path of the folder containing one subfolder by sample. Each subfolder contains the Bruker files of this sample.

which.spectra

If there is more than one spectrum by sample, which is the spectrum to import (either always the first one with which.spectra = "first", always the last one with which.spectra = "last" or a vector of length the number of spectra that specifies the number of each spectrum to import). Default to "last".

baseline.correction

Logical. If TRUE a baseline correction is applied for each spectrum (Wang et al (2013)). Default to TRUE.

alignment

Logical. If TRUE a peak alignment is applied between all spectra (Vu et al (2011)). Default to FALSE.

ppm.grid

Numeric vector of a unique grid (definition domain) for all spectra (in ppm). Default to NULL (in which case, the default grid of the pure library is used).

sample.names

Character vector of sample names. Default to NULL (in which case, folder names are used).

ncores

Number of cores used in parallel evaluation. Default to 1.

...

Further arguments to be passed to the function alignment 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 by the area under the curve.

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.

Vu, T. N., Valkenborg, D., Smets, K., Verwaest, K. A., Dommisse, R., Lemiere, F., ... & Laukens, K. (2011). An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics, 12(1), 405.

See Also

baselineCorrection normalisation alignment

Examples

current_path <- system.file("extdata", "example_spectra", package = "ASICS")
spectra_data <- importSpectraBruker(current_path)

[Package ASICS version 1.0.1 Index]