\HeaderA{BCXmotifs}{The Xmotifs Bicluster algorithm}{BCXmotifs}
\aliasA{BCXmotifs-class}{BCXmotifs}{BCXmotifs.Rdash.class}
\aliasA{biclust,matrix,BCXmotifs-method}{BCXmotifs}{biclust,matrix,BCXmotifs.Rdash.method}
\aliasA{Xmotif}{BCXmotifs}{Xmotif}
\keyword{cluster}{BCXmotifs}
\keyword{classif}{BCXmotifs}
\begin{Description}\relax
Performs XMotifs Biclustering based on the framework by Murali and Kasif (2003). Searches for a submatrix where each row as a similar motif through all columns.
The Algorihm needs a discret matrix to perform.
\end{Description}
\begin{Usage}
\begin{verbatim}

## S4 method for signature 'matrix, BCXmotifs':
biclust(x, method=BCXmotifs(), ns=10, nd=10, sd=5, alpha=0.05, number=100)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] Data Matrix.
\item[\code{method}] Here BCXmotifs, to perform Xmotifs algorithm
\item[\code{ns}] Number of rows choosen.
\item[\code{nd}] Number of repetitions.
\item[\code{sd}] Sample size in repetitions.
\item[\code{alpha}] Scaling factor for column result.
\item[\code{number}] Number of bicluster to be found.
\end{ldescription}
\end{Arguments}
\begin{Value}
Returns an object of class \code{Biclust}.
\end{Value}
\begin{Section}{Extends}
Class \code{"\LinkA{BiclustMethod}{BiclustMethod.Rdash.class}"}, directly.
\end{Section}
\begin{Author}\relax
Sebastian Kaiser 
\email{sebastian.kaiser@stat.uni-muenchen.de}
\end{Author}
\begin{References}\relax
Murali, T. \& Kasif, S. 
Extracting Conserved Gene Expression Motifs from Gene Expression Data 
Pacific Symposium on Biocomputing, sullivan.bu.edu, 
2003, 8, 77-88
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{biclust}{biclust}}, \code{\LinkA{Biclust}{Biclust}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(BicatYeast)
x<-discretize(BicatYeast)
res <- biclust(x, method=BCXmotifs(), ns=20, nd=20, sd=5, alpha=0.01, number=10)
res
\end{ExampleCode}
\end{Examples}

