ASICS {ASICS} | R Documentation |
Quantification of 1D 1H NMR spectra with ASICS method using a library of pure metabolite spectra. The method is presented in Tardivel et al. (2017).
ASICS(spectra_obj, exclusion.areas = matrix(c(4.5, 5.1), ncol = 2), max.shift = 0.02, pure.library = NULL, threshold.noise = 0.02, combine = TRUE, seed = 1234, ncores = 1, verbose = TRUE)
spectra_obj |
An object of class Spectra obtained with the function createSpectra. |
exclusion.areas |
Definition domain of spectra that has to be excluded for the quantification (ppm). By default, the water region is excluded (4.5-5.1 ppm). |
max.shift |
Maximum chemical shift allowed (in ppm). Default to 0.02. |
pure.library |
An object of class PureLibrary containing
the reference spectra (pure metabolite spectra). If |
threshold.noise |
Threshold for signal noise. Default to 0.02. |
combine |
Logical. If |
seed |
Random seed to control randomness in the algorithm (used in the estimation of the significativity of a given metabolite concentration). |
ncores |
Number of cores used in parallel evaluation. Default to
|
verbose |
A boolean value to allow print out process information. |
An object of type ASICSResults containing the quantification results.
Tardivel P., Canlet C., Lefort G., Tremblay-Franco M., Debrauwer L., Concordet D., Servien R. (2017). ASICS: an automatic method for identification and quantification of metabolites in complex 1D 1H NMR spectra. Metabolomics, 13(10): 109. https://doi.org/10.1007/s11306-017-1244-5
ASICSResults pure_library
createSpectra
# Import data and create object current_path <- system.file("extdata", package = "ASICS") spectra_data <- importSpectra(name.dir = current_path, name.file = "spectra_example.txt", type.import = "txt") spectra_obj <- createSpectra(spectra_data) # Estimation of relative quantification of Lactate and L-Alanine to_exclude <- matrix(c(4.5, 10), ncol = 2) pure_lib <- pure_library[getSampleName(pure_library) %in% c("Lactate", "L-Alanine")] resASICS <- ASICS(spectra_obj[1], exclusion.areas = to_exclude, pure.library = pure_lib, combine = FALSE)