\HeaderA{modelSLGI}{Permutation model for assessing synthetic genetic interactions in
cellular organizational units.}{modelSLGI}
\keyword{data}{modelSLGI}
\keyword{manip}{modelSLGI}
\begin{Description}\relax
Permutation model for assessing synthetic genetic interactions within
and between cellular organizational units such as multi-protein complexes.
\end{Description}
\begin{Usage}
\begin{verbatim}
modelSLGI(iMat, universe, interactome,  type="intM", perm=50)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{iMat}] Adjacency matrix reporting genetic interactions. Each entry has value 0 or 1,
representing positive or negative interaction of corresponding pairs
of row and column.
\item[\code{universe}] character vector of the names of the tested
genes, e.g., names of the genes on the synthetic genetic array
(SGA) used by Tong et al.
\item[\code{interactome}] Adjacency matrix where row are genes and
columns are cellular organizational units. Each entry has
value 0 or 1, for absence or presence of a gene in a complex.
\item[\code{type}] Character vector of value "intM" (Default) or
"interactome" to either perform the test based on to the genetic interaction matrix or the
interactome, respectively.
\item[\code{perm}] Number of permutations to apply. Default is 50.
\end{ldescription}
\end{Arguments}
\begin{Value}
Interaction matrix between cellular organizational units.
\end{Value}
\begin{Author}\relax
N. LeMeur
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{getInteraction}{getInteraction}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
 data(ScISIC)
 data(Atong)
 data(SGA)
 model <-  modelSLGI(Atong, universe= SGA, interactome=ScISIC,
type="intM", perm=2)
 \end{ExampleCode}
\end{Examples}

