\HeaderA{list.siggenes}{List of the significant genes}{list.siggenes}
\keyword{IO}{list.siggenes}
\keyword{file}{list.siggenes}
\begin{Description}\relax
Lists the genes called differentially expressed by the SAM analysis for
a specified value of the threshold \eqn{\Delta}{Delta}.
\end{Description}
\begin{Usage}
\begin{verbatim}
  list.siggenes(object, delta, file = "", gene.names = NULL, order = TRUE, 
  text = NULL, append = FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] a object of class SAM
\item[\code{delta}] a numeric value specifying the threshold \eqn{\Delta}{Delta}
in a SAM analysis
\item[\code{file}] a character string naming a file in which the output is stored.
If \code{""}, the significant genes will be shown in the console
\item[\code{gene.names}] a character vector containing the names of the genes. Needs
only to be specified, if the gene names were not specified in \code{sam} 
\item[\code{order}] If \code{TRUE}, the gene names will be ordered by their 
"significance"
\item[\code{text}] a character string specifying the heading of the gene list. By
default no heading is added to the gene list
\item[\code{append}] If \code{TRUE}, the output will be appended to \code{file}. If
\code{FALSE}, any existing file having the name \code{file} will be destroyed
\end{ldescription}
\end{Arguments}
\begin{Value}
A list of significant genes either shown in the console or stored in a file.
\end{Value}
\begin{Author}\relax
Holger Schwender, \email{holger.schw@gmx.de}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{SAM-class}{SAM.Rdash.class}},\code{\LinkA{sam}{sam}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}## Not run: 
  # Load the package multtest and the data of Golub et al. (1999)
  # contained in \pkg{multtest}.
  library(multtest)
  data(golub)

  # Perform a SAM analysis.
  sam.out<-sam(golub,golub.cl,B=100,rand=123)
  
  # List the genes called significant by SAM using Delta = 3.1.
  list.siggenes(sam.out,3.1,gene.names=golub.gnames[,2])
## End(Not run)\end{ExampleCode}
\end{Examples}