--- a +++ b/R/DLBCLdata-package.R @@ -0,0 +1,54 @@ +#' \pkg{DLBCLdata}: Automated and reproducible download and preprocessing of +#' DLBCL data +#' +#' @description +#' An R-package for reproducible and easily available gene expression profile +#' (GEP) datasets in Diffuse Large B-cell Lymphoma (DLBCL). +#' This package automatically downloads and preproceses the microarray data +#' using the manufacturer's or custom Brainarray chip definition files (CDF). +#' +#' The most important user function is \code{\link{downloadAndProcessGEO}} and +#' the functions documented from there. For more information, read the README +#' file \href{https://github.com/AEBilgrau/DLBCLdata}{here at GitHub.} +#' +#' @author +#' Anders Ellern Bilgrau\cr +#' Steffen Falgreen Larsen +#' @docType package +#' @name DLBCLdata-package +#' @aliases DLBCLdata-package DLBCLdata dlbcldata dlbcl DLBCL +#' @examples +#' # Overview of the curated available data: +#' print(DLBCL_overview[,-6]) +#' +#' # Overview of all functions in DLBCLdata +#' ls("package:DLBCLdata") +NULL + +#' Overview of available DLBCL data +#' +#' A \code{data.frame} of the manually checked and curated DLBCL datasets in +#' the \pkg{DLBCLdata}-package. +#' The \code{data.frame} gives information on the GEO number, a study +#' acronym, the expanded acronym, the principal author, the arraytypes +#' present in the study, and a full citation. +#' +#' @docType data +#' @name DLBCL_overview +#' @format +#' A \code{data.frame} giving information about the DLBCL studies with the +#' following columns:\cr +#' \describe{ +#' \item{\code{GSE}}{The accession number} +#' \item{\code{Study}}{A name or abbreviation of the study.} +#' \item{\code{FullName}}{The full name of the study.} +#' \item{\code{Author}}{The first author of the study.} +#' \item{\code{ArrayTypes}}{The array type(s) used for the gene expression profiles.} +#' \item{\code{Citationv}}{Citation information. Please double check the information +#' if the data is used.} +#' } +#' @keywords datasets, data +#' @examples +#' print(DLBCL_overview[,-6]) +#' #View(DLBCL_overview) +NULL