% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/2_geo_id.R
\name{geo_download}
\alias{geo_download}
\title{geo_download}
\usage{
geo_download(
  gse,
  by_annopbrobe = TRUE,
  simpd = TRUE,
  colon_remove = TRUE,
  download_timeout = getOption("timeout"),
  destdir = getwd(),
  n = 1
)
}
\arguments{
\item{gse}{GEO accession number or a path to a cached `.rds` or `.RData`
file containing an `ExpressionSet` or a list of `ExpressionSet` objects}

\item{by_annopbrobe}{whether to try the AnnoProbe cache first and fall back
to GEOquery::getGEO()}

\item{simpd}{whether to simplify phenotype data by dropping columns with a
single unique value}

\item{colon_remove}{whether to drop raw `characteristics_ch1*` columns
while keeping the derived `:ch1` phenotype column names intact}

\item{download_timeout}{timeout in seconds used for GEOquery fallback and
for mirror stall detection during the resumable download}

\item{destdir}{The destination directory for data downloads}

\item{n}{For data with more than one ExpressionSet, specify which one to analyze}
}
\value{
a list with `exp`, `pd`, `gpl`, and `group_candidates`, or `NULL`
  when the data cannot be read or downloaded
}
\description{
Download GEO expression data and return the expression matrix, phenotype
data, and platform information.
}
\details{
Cached `eSet` objects are stored as `.rds` files in `destdir`; legacy
`.Rdata` cache files are still readable, and incomplete cache files will be
kept so the download can resume automatically.
}
\examples{
\dontrun{
if(requireNamespace("Biobase",quietly = TRUE)){
  gse = "GSE42872"
  a = geo_download(gse,destdir=tempdir())
}
}
}
\seealso{
\code{\link{find_anno}}
}
\author{
Xiaojie Sun
}
