R/guidebook_data.R

In thomazbastiaanssen/Tjazi: Microbiome Oriented Compositional Data Toolkit

#' The curated and aggregated genus-level count table from the schizophrenia study for demonstration
#'
#' @description A genus-level count table for instructional purposes. Accessed using the curatedMetagenomicData R package
#'
#' @format A data.frame object with 162 rows, genera, and  171 columns, samples.
#' @source \url{https://doi.org/10.1038/s41467-020-15457-9}
#'
"counts"


#' The curated Gut-Brain modules count table from the schizophrenia study for demonstration
#'
#' @description A Gut-Brain modules count table for instructional purposes. Accessed using the curatedMetagenomicData R package
#'
#' @format A data.frame object with 43 rows, Gut-Brain modules, and  171 columns, samples.
#' @source \url{https://doi.org/10.1038/s41467-020-15457-9}
#'
"GBMs"


#' The curated Gut-Metabolic modules count table from the schizophrenia study for demonstration
#'
#' @description A Gut-Metabolic modules count table for instructional purposes. Accessed using the curatedMetagenomicData R package
#'
#' @format A data.frame object with 98 rows, Gut-Metabolic, and  171 columns, samples.
#' @source \url{https://doi.org/10.1038/s41467-020-15457-9}
#'
"GMMs"


#' A snippet of the metadata from the schizophrenia study
#'
#' @description Contains the per-sample information for the samples from the schizophrenia study. Accessed using the curatedMetagenomicData R package
#'
#' @format A data.frame object with 171 rows, samples, and 10 columns, denoting sample ID, schizophrenia status, sex, BMI, smoking status and some additional information from the original metadata.
#' @source \url{https://doi.org/10.1038/s41467-020-15457-9}
#'
"metadata"


#' A snippet of the dietary intake from the schizophrenia study
#'
#' @description Contains the per-sample dietary intake information for the participants from the schizophrenia study. Found in "Supplementary Data 1" on the journal website.
#'
#' @format A data.frame object with 171 rows, samples, and 5 columns, dietary categories, for which we have frequencies ranging from 'hardly' to 'every day'.
#' @source \url{https://doi.org/10.1038/s41467-020-15457-9}
#'
"diet"