| from_ASICS_to_PHOENICS {phoenics} | R Documentation |
Prepare quantification data from ASICS outputs
Description
Prepare quantification data from ASICS outputs for
test_pathway. In short, it replaces metabolite names by metabolites
KEGG codes and transposes the matrix to have samples in rows and metabolites
in columns.
Usage
from_ASICS_to_PHOENICS(quantif)
Arguments
quantif |
output matrix of |
Value
A matrix of quantification with samples in rows and metabolites in
columns, properly formatted for test_pathway
Author(s)
Camille Guilmineau <camille.guilmineau@inrae.fr>
Remi Servien <remi.servien@inrae.fr>
Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
References
Lefort G., Liaubet L., Canlet C., Tardivel P., P\'ere M.C., Quesnel H., Paris A., Iannuccelli N., Vialaneix N. Servien R. (2019). ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra. Bioinformatics, 35(21): 4356–4363. doi:10.1093/bioinformatics/btz248
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. doi:10.1007/s11306-017-1244-5
Examples
data("MTBLS422")
quantif <- from_ASICS_to_PHOENICS(quantif)