AlpsNMR allows you to import NMR spectra into R and provides automated and efficient signal processing for untargeted NMR metabolomics.
Details
The following functions can be combined with the pipe. They create or modify the nmr_dataset object.
There are also functions to extract the metadata and submit the samples to irods, see the example below.
The nmr_dataset object is essentially a list, so it is easy to access its components for further analysis.
Author
Maintainer: Sergio Oller Moreno sergioller@gmail.com (ORCID)
Authors:
Ivan Montoliu Roura Ivan.MontoliuRoura@rd.nestle.com
Francisco Madrid Gambin fmadrid@ibecbarcelona.eu (ORCID)
Luis Fernandez lfernandez@ibecbarcelona.eu (ORCID)
Héctor Gracia Cabrera hgracia@ibecbarcelona.eu
Santiago Marco Colás smarco@ibecbarcelona.eu (ORCID)
Other contributors:
Laura López Sánchez [contributor]
Nestlé Institute of Health Sciences [copyright holder]
Institute for Bioengineering of Catalonia [copyright holder]
Miller Jack jack.miller@physics.org (ORCID) (Autophase wrapper, ASICS export) [contributor]
Examples
dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR")
dataset <- nmr_read_samples_dir(dir_to_demo_dataset)
my_nmr_dataset <- dataset %>%
nmr_interpolate_1D(axis = c(0.4, 10)) %>%
nmr_exclude_region(exclude = list(water = c(4.6, 5))) %>%
nmr_normalize(method = "pqn") %>%
plot()
#> Warning: There are not enough samples for reliably estimating the median spectra
#> ℹ The Probabalistic Quotient Normalization requires several samples to compute the median spectra. Your number of samples is low
#> ℹ Review your peaks before and after normalization to ensure there are no big distortions