% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data_import.R
\name{load.geo.soft}
\alias{load.geo.soft}
\title{Load GEO Dataset from SOFT File}
\usage{
load.geo.soft(file.path = NULL, accession = NULL, log.transform = FALSE)
}
\arguments{
\item{file.path}{Character. Path to a local GEO SOFT file. If the file does
not exist and \code{accession} is provided, the dataset is downloaded
automatically.}

\item{accession}{Character. GEO accession ID (e.g., \code{"GDS507"}). Only
used when \code{file.path} does not exist. Default is \code{NULL}.}

\item{log.transform}{Logical. Whether to apply a log2 transformation to the
expression matrix during import. Default is \code{FALSE}.}
}
\value{
An \code{ExpressionSet} object for use with \code{extract.expression()}.
}
\description{
Imports a GEO dataset and converts it into a structured ExpressionSet object.
If a local SOFT file is found at \code{file.path} it is loaded directly.
Otherwise the dataset is downloaded from NCBI GEO using \code{accession} and
cached in \code{tempdir()}.
}
\examples{
\donttest{
# Download automatically if not found locally
eset <- load.geo.soft("GDS507.soft", accession = "GDS507", log.transform = TRUE)

# Download without a local file at all
eset <- load.geo.soft(NULL, accession = "GDS507", log.transform = TRUE)
}

}
