R/cobradata_example.R

In iCOBRA: Comparison and Visualization of Ranking and Assignment Methods

#' Example data set with three differential gene expression methods
#'
#' A data set consisting of p-values, adjusted p-values and estimated absolute
#' log fold changes (in the 'scores' slot) obtained by three methods for
#' differential expression analysis of RNA-seq data, applied to a small
#' synthetic data set of 3,858 human genes. The values are stored in a
#' \code{COBRAData} object together with a 'truth' data frame containing the
#' true differential expression status for each gene as well as various
#' additional annotations such as the true log fold change, the number of
#' isoforms of the gene and the average expression level.
#'
#' @format A \code{COBRAData} object with five slots:
#' \describe{
#'   \item{pval}{data frame with p-values for 2,399 genes, from three different
#'   methods.}
#'   \item{padj}{data frame with adjusted p-values for 2,399 genes, from two
#'   different methods.}
#'   \item{sval}{empty data frame}
#'   \item{score}{data frame with estimated absolute log fold changes for 2,399
#'   genes, from three different methods.}
#'   \item{truth}{data frame with true differential expression status (status
#'   column), the number of isoforms (n_isoforms column), the true absolute log
#'   fold change (logFC and logFC_cat columns) and average expression level 
#'   (expr and expr_cat columns) for 3,858 genes.}
#'   }
#' @return A \code{COBRAData} object.
"cobradata_example"