R/data.R

In microbiome: Microbiome Analytics

#' @title Probiotics Intervention Data
#' @description The peerj32 data set contains high-through profiling data from 
#' 389 human blood serum lipids and 130 intestinal genus-level bacteria from 
#' 44 samples (22 subjects from 2 time points; before and after 
#' probiotic/placebo intervention). The data set can be used to investigate 
#' associations between intestinal bacteria and host lipid metabolism. 
#' For details, see \url{http://dx.doi.org/10.7717/peerj.32}.
#' @name peerj32
#' @docType data
#' @author Leo Lahti \email{microbiome-admin@@googlegroups.com} 
#' @references Lahti et al. (2013) PeerJ 1:e32
#' \url{http://dx.doi.org/10.7717/peerj.32}
#' @usage data(peerj32)
#' @return Loads the data set in R.
#' @format List of the following data matrices as described in detail in
#' Lahti et al. (2013):
#' \itemize{
#' \item lipids: Quantification of 389 blood serum lipids across 44 samples
#' \item microbes: Quantification of 130 genus-like taxa across 44 samples
#' \item meta: Sample metadata including time point, sex, subjectID,
#' sampleID and treatment group (probiotic LGG / Placebo)
#' \item phyloseq The microbiome data set converted into a
#' \code{\link{phyloseq-class}} object.
#' }
#' 
#' @keywords data
NULL


#' @title Diet Swap Data 
#' @description The diet swap data set represents a study with African
#' and African American groups undergoing a two-week diet swap.
#' For details, see
#' \url{dx.doi.org/10.1038/ncomms7342}.
#' @name dietswap
#' @return Loads the data set in R.
#' @details The data is also available for download from the Data Dryad
#' repository \url{http://datadryad.org/resource/doi:10.5061/dryad.1mn1n}. 
#' @docType data
#' @author Leo Lahti \email{microbiome-admin@@googlegroups.com} 
#' @references 
#' O'Keefe et al. Nature Communications 6:6342, 2015.
#' \url{dx.doi.org/10.1038/ncomms7342}
#' To cite the microbiome R package, see citation('microbiome') 
#' @usage data(dietswap) 
#' @format The data set in \code{\link{phyloseq-class}} format.  
#' @keywords data
NULL



#' @title HITChip Atlas with 1006 Western Adults
#' @description This data set contains genus-level microbiota profiling with
#' HITChip for 1006 western adults with no reported health complications,
#' reported in Lahti et al. (2014) \url{https://doi.org/10.1038/ncomms5344}.
#' @name atlas1006
#' @details The data is also available for download from the Data Dryad
#' \url{http://doi.org/10.5061/dryad.pk75d}. 
#' @docType data
#' @author Leo Lahti \email{microbiome-admin@@googlegroups.com}
#' @return Loads the data set in R.
#' @references 
#' Lahti et al. Tipping elements of the human intestinal ecosystem. 
#' Nature Communications 5:4344, 2014.
#' To cite the microbiome R package, see citation('microbiome') 
#' @usage data(atlas1006) 
#' @format The data set in \code{\link{phyloseq-class}} format.  
#' @keywords data
NULL


#' @title HITChip Taxonomy
#' @description HITChip taxonomy table.
#' @name hitchip.taxonomy
#' @docType data
#' @return Loads the data set in R.
#' @author Leo Lahti \email{microbiome-admin@@googlegroups.com} 
#' @references 
#' Lahti et al. Tipping elements of the human intestinal ecosystem. 
#' Nature Communications 5:4344, 2014.
#' To cite the microbiome R package, see citation('microbiome') 
#' @usage data(hitchip.taxonomy)
#' @format List with the element 'filtered', including a simplified version
#' of the HITChip taxonomy.
#' @keywords data
NULL