Add data documentation

R/data.R

@@ -22,8 +22,8 @@
 #' @details The raw dataset have been made available on MetaboLights (with the
 #' id MTBLS422 \url{https://www.ebi.ac.uk/metabolights/editor/MTBLS422}) by
 #' [Choo \emph{et al.}, 2017]. Metabolites quantifications were obtained
-#' based on the raw signal using \link[ASICS] package. Pathways were obtained
-#' using \link[KEGGREST] package. The datasets provided for the example
+#' based on the raw signal using \code{ASICS} package. Pathways were obtained
+#' using \code{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.,
@@ -47,6 +47,6 @@
 #' 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.
 #'
-
+NULL
 
 

man/MTBLS422.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{MTBLS422}
+\alias{MTBLS422}
+\title{Dataset "MTBLS422"}
+\format{
+3 datasets are provided: \itemize{
+\item \code{quantif}: a data frame with 10 rows (metabolites name) and 11
+columns (samples id), which corresponds to the metabolites quantifications
+in the samples.
+\item \code{pathways}: a data frame with 11 rows and 4 columns, which
+contains informations about pathways and their metabolites.
+\item \code{design}: a data frame with 11 rows (samples id) and 4 columns
+(id and effects to be added in the model).
+}
+}
+\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.
+}
+\details{
+The raw dataset have been made available on MetaboLights (with the
+id MTBLS422 \url{https://www.ebi.ac.uk/metabolights/editor/MTBLS422}) by
+[Choo \emph{et al.}, 2017]. Metabolites quantifications were obtained
+based on the raw signal using \code{ASICS} package. Pathways were obtained
+using \code{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. \emph{mSphere}, \strong{2}(1)
+\url{https://doi.org/10.1128/msphere.00005-17}
+ 
+Lefort G., Liaubet L., Canlet C., Tardivel P., Père 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.
+\emph{Bioinformatics}, \strong{35}(21): 4356–4363.
+\url{https://doi.org/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. \emph{Metabolomics}, \strong{13}(10): 109.
+\url{https://doi.org/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.
+}