\HeaderA{getInteraction}{Count genetic interactions within and between cellular
organizational units}{getInteraction}
\keyword{methods}{getInteraction}
\begin{Description}\relax
Count the number of genetic interactions within and between the elements of the interactome.
\end{Description}
\begin{Usage}
\begin{verbatim}getInteraction(iMat, universe, interactome)\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{iMat}] Interaction matrix. Each entry has value 0 or 1,
representing positive or negative interaction of corresponding pairs
of row and column, respectively.
\item[\code{universe}] Character vector of gene names, e.g., array genes used
in synthetic genetic array experiments (SGA)
\item[\code{interactome}] Adjacency matrix where row are gene names and
columns are cellular organizational units. 
\end{ldescription}
\end{Arguments}
\begin{Value}
The returned value is a list of 2 matrices:
\begin{ldescription}
\item[\code{bwMat}] A interaction matrix that corresponds to the  cellular
organizational units interaction matrix where row and columns a
organizational units names and the value inside the
matrix are the number of genetic interactions they share.
\item[\code{CDs}] Subset of the input interactome that shares interactions.
\end{ldescription}
\end{Value}
\begin{Author}\relax
N. LeMeur
\end{Author}
\begin{Examples}
\begin{ExampleCode}
##Create the genetic interaction matrix
gInt <- sample(c(0, 1), 25, TRUE)
iMat  <- matrix(gInt, nrow=5, ncol=5, dimnames=list(letters[1:5],letters[4:8]))

##Create the interactome
cInt <- sample(c(0,1),30, TRUE)
interactome  <- matrix(cInt, nrow=6, ncol=5,dimnames=list(letters[2:7],LETTERS[1:5]))

## Reduce the genetic interaction matrix to match the gene present in
## the interactome
reducediMat <- gi2Interactome(iMat, interactome)

## Get the interaction
prey <- letters[1:20]
myInteraction <- getInteraction(reducediMat, prey, interactome)
\end{ExampleCode}
\end{Examples}

