This user's guide provides an overview of the package ASICS
. ASICS
is a
fully automated procedure to identify and quantify metabolites in $^1$H NMR
spectra of biological mixtures. It will enable empowering NMR-based metabolomics
by quickly and accurately helping experts to obtain metabolic profiles.
library(ASICS)
A dataset with spectra of 175 pure metabolites is available in the package. It is automatically loaded at package start and available metabolites are displayed with:
head(pure_library$name, n = 20)
The identification and the quantification are carried out using only one
function ASICS
directly from raw files (Bruker files):
# part of the spectrum to exclude (water) to_exclude <- matrix(c(4.5,5.1,5.5,6.5), ncol = 2, byrow = TRUE) result <- ASICS(path = system.file("extdata", "example_spectra", "AG_faq_Beck01", package = "ASICS"), exclusion.areas = to_exclude) result
The quality of the results can be assessed by stacking the original and the recomposed spectra on one plot. A pure metabolite spectrum can also be added for visual comparison.
plot(result, xmin = 1, xmax = 1.5, ymax = 10, add_metab = "Lactate")
Relative concentrations of identified metabolites are saved in:
head(present_metabolites(result), 10)
Usually, many spectra are available for one experience. With the
ASICS_multiFiles
function, quantification is launched on all spectra present
in the specified folder (name.dir
). The arguments of this function are the
same than for ASICS
function with the addition of ncores
for parallel
computation (if wanted).
res_multi <- ASICS_multiFiles(name.dir = system.file("extdata", "example_spectra", package = "ASICS"), exclusion.areas = to_exclude, ncores = 4)
For further analyses, it is possible to extract concentrations of all spectra in a data-frame:
quantification <- extract_concentrations(res_multi) head(quantification)
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
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