\HeaderA{normInteraction}{Normalize a matrix of biological interactions}{normInteraction}
\keyword{data}{normInteraction}
\keyword{manip}{normInteraction}
\begin{Description}\relax
Normalize a square matrix of biological interactions according to the number
of possible interactions between each biological complex.
\end{Description}
\begin{Usage}
\begin{verbatim}normInteraction(data, genename, interactome)\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{data}] Square Matrix of biological complexes that shares one or
more genes(proteins)
\item[\code{genename}] Character vector of the gene names that possibly
create interactions between complexes
\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, e.g., \code{\LinkA{ScISI}{ScISI}}
\end{ldescription}
\end{Arguments}
\begin{Value}
Square matrix of biological complexes linked by one or more
interacting proteins and normalized by the possible number of
interactions between each complex.
\end{Value}
\begin{Author}\relax
N. LeMeur
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{getInteraction}{getInteraction}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(Atong)
data(ScISIC)
data(SGA)
SLa2 <- gi2Interactome(Atong, ScISIC)
## Search for synthetic lethal interaction
compM <- getInteraction(SLa2, SGA, ScISIC)
## Normalize
normIntComplex<- normInteraction(compM$bwMat, SGA, ScISIC)
\end{ExampleCode}
\end{Examples}

