phoenics (version 0.3)

MTBLS422: Dataset "MTBLS422"

Description

Metabolites quantifications, associated metabolic pathways and experimental design to characterize the effects of two clinically important antibiotic treatments, ciprofloxacin and vancomycin-imipenem on mice.

Format

3 datasets are provided:

• quantif: a data frame with 10 rows (metabolites name) and 11 columns (samples id), which corresponds to the metabolites quantifications in the samples.

• pathways: a data frame with 11 rows and 4 columns, which contains informations about pathways and their metabolites.

• design: a data frame with 11 rows (samples id) and 4 columns (id and effects to be added in the model).

Details

The raw dataset have been made available on MetaboLights (with the id MTBLS422 https://www.ebi.ac.uk/metabolights/editor/MTBLS422) by [Choo et al., 2017]. Metabolites quantifications were obtained based on the raw signal using ASICS package. Pathways were obtained using KEGGREST package. The datasets provided for the example are a subset of the original dataset.

References

Choo J. M., Kanno T., Zain N. M. M., Leong L. E. X., Abell G. C. J., Keeble J. E., Bruce K. D., Mason A. J., Rogers G. B. (2017). Divergent relationships between fecal microbiota and metabolome following distinct antibiotic-induced disruptions. mSphere, 2(1) tools:::Rd_expr_doi("10.1128/msphere.00005-17")

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. 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. tools:::Rd_expr_doi("10.1007/s11306-017-1244-5")

Tenenbaum D., Maintainer B. (2022). KEGGREST: Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG). R package version 1.38.0.

Examples

data(MTBLS422)
# \donttest{
design[1:5, ]
pathways[1:5, ]
quantif[1:5, 1:5]
# }