R/ex-data.R

In scDD: Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

#' Data: Toy example data list 
#'
#' Toy example data list (one item for each of two conditions) for 100 genes
#'  to illustrate how to use the function
#'  \code{\link{preprocess}}.  
#'
#' @name scDatExList
#'
#' @docType data
#'
#' @usage data(scDatExList)
#'
#' @format A list of two matrices (one for each of two conditions) labeled 
#' "C1" and "C2".  Each matrix contains data for 100 genes
#'   and a variable number of samples (78 in C1 and 64 in C2).
#'   
#' @return An RData object, see Format section for details
#'   
#' @references Korthauer KD, Chu LF, Newton MA, Li Y, Thomson J, Stewart R, 
#' Kendziorski C. A statistical approach for identifying differential 
#' distributions
#' in single-cell RNA-seq experiments. Genome Biology. 2016 Oct 25;17(1):222. 
#' \url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-
#' 1077-y}
#'
#' @keywords datasets
#'
#' @examples 
#' 
#' # load toy example data list 
#' data(scDatExList)
#'
NULL


#' Data: Toy example data
#'
#' Toy example data in \code{SingleCellExperiment} format for 500 
#' genes to illustrate how to generate simulated data from example data
#'  using \code{\link{simulateSet}}.  
#'
#' @name scDatEx
#'
#' @docType data
#'
#' @usage data(scDatEx)
#'
#' @format An object of class \code{SingleCellExperiment} containing
#'  data for 500 genes for 142 samples
#'  (78 from condition 1 and 64 from condition 2).  Condition labels (1 or 2)
#'   are stored in the colData slot. The assays slot contains both normcounts
#'   and counts for illustration, but these objects are identical.
#' 
#' @return An RData object, see Format section for details
#'   
#' @references Korthauer KD, Chu LF, Newton MA, Li Y, Thomson J, Stewart R, 
#' Kendziorski C. A statistical approach for identifying differential 
#' distributions
#' in single-cell RNA-seq experiments. Genome Biology. 2016 Oct 25;17(1):222. 
#' \url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-
#' 1077-y}   
#'
#' @keywords datasets
#'
#' @examples 
#' 
#' # load toy example data 
#' data(scDatEx) 
NULL


#' Data: Toy example of simulated data
#'
#' Toy example data in \code{SingleCellExperiment} format for 500 
#' genes to illustrate how to generate simulated data from example data
#'  using \code{\link{simulateSet}}.  Contains 5 genes from each category 
#'  (DE, DP, DM, DB, EE, and EP).
#'
#' @name scDatExSim
#'
#' @docType data
#'
#' @usage data(scDatExSim)
#'
#' @format An object of class \code{SingleCellExperiment} containing 
#' data for 30 genes for 200 samples
#'  (100 from condition 1 and 100 from condition 2).  Condition labels (1 or 2)
#'   are stored in the colData slot.  
#'  Row names of the assayData slot contain the two letter category label that
#'   the gene was simulated from (e.g.  'EE', 'DB', ...)
#'  along with the row number (1-30).
#'    
#' @return An RData object, see Format section for details
#'     
#' @references Korthauer KD, Chu LF, Newton MA, Li Y, Thomson J, Stewart R, 
#' Kendziorski C. A statistical approach for identifying differential 
#' distributions
#' in single-cell RNA-seq experiments. Genome Biology. 2016 Oct 25;17(1):222. 
#' \url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-
#' 1077-y}
#'
#' @keywords datasets
#'
#' @examples 
#' 
#' # load toy example of simulated data
#' data(scDatExSim)
NULL