% 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

}