--- a
+++ b/man/downloadAndProcessGEO.Rd
@@ -0,0 +1,50 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/downloadAndProcessGEO.R
+\name{downloadAndProcessGEO}
+\alias{downloadAndProcessGEO}
+\title{Download GEO dataset and preprocess it}
+\usage{
+downloadAndProcessGEO(geo_nbr, destdir = getwd(), ..., clean = FALSE,
+  verbose = TRUE)
+}
+\arguments{
+\item{geo_nbr}{The GEO ascession number.}
+
+\item{destdir}{The destination dir of the downloaded files.}
+
+\item{...}{Arguments passed to \code{\link{preprocessCELFiles}}}
+
+\item{clean}{Should the strictly unnessesary files be deleted?}
+
+\item{verbose}{Signal the process.}
+}
+\value{
+Creates a folder with the downloaded and processed files.
+  The processed files are saved as an \code{.Rds} object named
+  after the used parameters.
+  Invisibly returns the saved object.
+}
+\description{
+Functionality for automatically downloading, RMA preprocessing the array
+data and formatting the phenotype data, and saving the results in a
+\code{.Rds} file.
+}
+\note{
+The function will overwrite existing files in the \code{destdir}.
+
+  Arguments after \code{\dots} must be named.
+}
+\examples{
+\dontrun{
+print(DLBCL_overview)
+geo_nbr <- DLBCL_overview[6,1]
+res <- downloadAndProcessGEO(geo_nbr = geo_nbr, cdf = "brainarray",
+                             target = "ENSG", clean = FALSE)
+head(exprs(res$es$Batch1))
+}
+}
+\author{
+Anders Ellern Bilgrau,
+  Steffen Falgreen Larsen
+}
+