from_ASICS_to_PHOENICS: Prepare quantification data from ASICS outputs

In phoenics: Pathways Longitudinal and Differential Analysis in Metabolomics

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 ASICS quantification

Value

A matrix of quantification with samples in rows and metabolites in columns, properly formatted for test_pathway

Author(s)

Camille Guilmineau <[e-mail]>
Remi Servien <[e-mail]>
Nathalie Vialaneix <[e-mail]>

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. \Sexpr[results=rd]{tools:::Rd_expr_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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/s11306-017-1244-5")}

Examples

data("MTBLS422")
quantif <- from_ASICS_to_PHOENICS(quantif)

phoenics documentation built on Sept. 11, 2024, 6:32 p.m.