\name{automaticNetworkScreeningGS}
\alias{automaticNetworkScreeningGS}
\title{ One-step automatic network gene screening with external gene significance }
\description{
  This function performs gene screening based on external gene significance and their network properties.  
}
\usage{
automaticNetworkScreeningGS(
     datExpr, GS, 
     power = 6, networkType = "unsigned", 
     detectCutHeight = 0.995, minModuleSize = min(20, ncol(as.matrix(datExpr))/2), 
     datME = NULL)
}
\arguments{
  \item{datExpr}{ data frame containing the expression data, columns corresponding to genes and rows to
samples }

  \item{GS}{ vector containing gene significance for all genes given in \code{datExpr} }

  \item{power}{ soft thresholding power used in network construction }

  \item{networkType}{ character string specifying network type. Allowed values are (unique abbreviations
of) \code{"unsigned"}, \code{"signed"}, \code{"hybrid"}. } 

  \item{detectCutHeight}{ cut height of the gene hierarchical clustering dendrogram. See
\code{cutreeDynamic} for details. }
  \item{minModuleSize}{ minimum module size to be used in module detection procedure. }
  \item{datME}{ optional specification of module eigengenes. A data frame whose columns are the module
eigengenes. If given, module analysis will not be performed. }
}
\details{
  Network screening is a method for identifying genes that have a high gene significance and are members
of important modules at the same time. 
  If \code{datME} is given, the function calls \code{\link{networkScreeningGS}} with the default
parameters. If \code{datME} is not given, module eigengenes are first calculated using network analysis
based on supplied parameters.
}
\value{
  A list with the following components:
  \item{networkScreening}{a data frame containing results of the network screening procedure. See
\code{\link{networkScreeningGS}} for more details.}
  \item{datME}{ calculated module eigengenes (or a copy of the input \code{datME}, if given).}
  \item{hubGeneSignificance}{ hub gene significance for all calculated modules. See
\code{\link{hubGeneSignificance}}. }
}
\author{ Steve Horvath }
\seealso{ \code{\link{networkScreening}}, \code{\link{hubGeneSignificance}},
\code{\link{networkScreening}}, \code{\link[dynamicTreeCut]{cutreeDynamic}} }
\keyword{ misc }% __ONLY ONE__ keyword per line
