R/data.R

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

#' Test data
#'
#' Data from a Zackular, Joseph P., et al. "The gut microbiome modulates colon tumorigenesis." MBio 4.6 (2013): e00692
#' -13.
#'
#' @docType data
#'
#' @usage data("zackular2014")
#'
#' @format An object of class \code{"phyloseq"}.
#'
#' @keywords datasets
#' @references
#' \itemize{
#' \item{}{Zackular, Joseph P., et al. "The gut microbiome modulates colon
#' tumorigenesis." MBio 4.6 (2013): e00692-13.,
#' \url{https://mbio.asm.org/content/4/6/e00692-13.short}}
#' }
#' @examples
#' \dontrun{
#' library(microbiomeutilities)
#' data("zackular2014")
#' pseq <- zackular2014
#' print(zackular2014)
#' }
#'
"zackular2014"

#' Test data 2
#'
#' Data from a Stansfield J, Dozmorov M. "16s rRNA sequencing data 
#' from the Human Microbiome Project 2". Randomly choosen 13 particpants
#' with multiple timepoints for rectum samples.
#'
#' @docType data
#'
#' @usage data("hmp2")
#'
#' @format An object of class \code{"phyloseq"}.
#'
#' @keywords datasets
#' @references
#' \itemize{
#' \item{}{Stansfield J, Dozmorov M (2019). HMP2Data: 16s rRNA sequencing data 
#' from the Human Microbiome Project 2. R package version 1.1.0,
#' \url{	https://bioconductor.org/packages/HMP2Data/}}
#' }
#' @examples
#' \dontrun{
#' library(microbiomeutilities)
#' data("hmp2")
#' pseq <- hmp2
#' print(hmp2)
#' }
#'
"hmp2"