| 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, seed = 1234, ncores = 1)
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. |
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
|
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 <- file.path(system.file("extdata", package = "ASICS"),
"spectra_example.txt")
spectra_data <- read.table(current_path, header = TRUE, row.names = 1)
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)