importSpectraBruker {ASICS} | R Documentation |
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.
importSpectraBruker(name.dir, which.spectra = "last", baseline.correction = TRUE, alignment = FALSE, ppm.grid = NULL, sample.names = NULL, ncores = 1, ...)
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 |
baseline.correction |
Logical. If |
alignment |
Logical. If |
ppm.grid |
Numeric vector of a unique grid (definition domain) for all
spectra (in ppm). Default to |
sample.names |
Character vector of sample names. Default to |
ncores |
Number of cores used in parallel evaluation. Default to
|
... |
Further arguments to be passed to the function
|
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.
A data frame with spectra in columns and chemical shifts (in ppm) in rows.
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.
baselineCorrection
normalisation
alignment
current_path <- system.file("extdata", "example_spectra", package = "ASICS") spectra_data <- importSpectraBruker(current_path)