R/data.R

In microsud/jeevanuDB: jeevanuDB: Example data sets for microbiome R pkg

#' @title emp_human
#' @description The emp_human data set contains high-through taxonomic profiling data from
#' 160 samples which is a small subet from the Earth Microbiome Project. 30 feces, 23 mucus,
#' 56 saliva and 51 sebum samples with ASV-level counts
#' as would be expected for denoising algorithms.
#' #' NOTE: These are only test datasets.
#' @name emp_human
#' @return Loads the data set in R.
#' @source https://www.nature.com/articles/nature24621
#' @docType data
#' @author Sudarshan Shetty \email{sudarshanshetty9@gmail.com}
#' @references Thompson LR et al. (2017) A communal catalogue reveals Earth’s multiscale microbial diversity
#' \url{https://www.nature.com/articles/nature24621}
#' @usage data(emp_human)
#' @format phyloseq object
#' @keywords data
"emp_human"

#' @title moving_pictures
#' @description The moving_pictures data set contains high-through taxonomic profiling data from
#' 1966 samples from two F4 (saliva n= 135, skin n= 268, stool n= 131) and M3 (saliva n= 373, skin n= 723, stool n= 336)
#' subjects which is a subet from the Earth Microbiome Project and samples from
#' the moving pictures study by . The ASV-level counts as would be expected for denoising algorithms.
#' NOTE: These are only test datasets.
#' @name moving_pictures
#' @return Loads the data set in R.
#' @docType data
#' @source https://www.nature.com/articles/nature24621
#' @author Sudarshan Shetty \email{sudarshanshetty9@gmail.com}
#' @references
#' \itemize{
#' \item{}{Thompson, Luke R., et al. "A communal catalogue reveals Earth’s multiscale microbial diversity." Nature 551, no. 7681 (2017): 457-463.}
#' \item{}{Caporaso, J. Gregory, et al. "Moving pictures of the human microbiome." Genome biology 12, no. 5 (2011): R50.}
#' \item{}{To cite the package, see citation('jeevanuDB')}
#' }
#' @usage data(moving_pictures)
#' @format phyloseq object
#' @keywords data
"moving_pictures"