This vignette 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 spectrum 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:
present_metabolites(result)
More details on ASICS functionnalities can be obtain in the user's guide :
ASICSUsersGuide()
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
This vignette has been created with the following system configuration
sessionInfo()
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.