\HeaderA{iSummary}{Summarize cellular organizational units sharing genetic interaction}{iSummary}
\keyword{data}{iSummary}
\keyword{manip}{iSummary}
\begin{Description}\relax
Summarize the cellular organizational units sharing genetic
interactions and display their GO annotation if available
\end{Description}
\begin{Usage}
\begin{verbatim}iSummary(iMat, n=10, reverse=FALSE)\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{iMat}] Comembership matrix of genes(proteins) that linked to
other genes(proteins) by any biological experiment, e.g., output of
the \code{getInteraction} function.
\item[\code{n}] Numeric threshold indicating the minimum number of genetic
interactions that a pair of cellular organizational unit must share.
\item[\code{reverse}] Logical, by default the function return a list of pair
of cellular organizational units where the name of each element is
the number of genetic interactions they share. If reverse is TRUE,
the output is a vector where the values are the number of
interactions and the names are the combination of the 2 cellular
organizational units.
\end{ldescription}
\end{Arguments}
\begin{Value}
The function print the result in the standard output but can also save it
in variable.

If \code{reverse} is FALSE the output is a list of pairs of cellular
organizational units where the name of each element is the number of
genetic interactions they share.

If \code{reverse} is TRUE the output is a vector where the values are
the number of interactions and the names are the combination of the 2
cellular organizational units.
\end{Value}
\begin{Author}\relax
N. LeMeur
\end{Author}
\begin{Examples}
\begin{ExampleCode}
data(Atong)
data(ScISIC)
data(SGA)
SLa2 <- gi2Interactome(Atong, ScISIC)
## Search for synthetic lethal interaction
compM <- getInteraction(SLa2, SGA, ScISIC)
## Display the tightly interacting pairs
largeInt <- iSummary(compM$bwMat,n=15)
\end{ExampleCode}
\end{Examples}

