\HeaderA{test2Interact}{Summarize genetic interactions within or between cellular
organizational units}{test2Interact}
\keyword{methods}{test2Interact}
\begin{Description}\relax
Summarize the genetic interactions within one cellular
organizational unit or between 2 cellular
organizational units.
\end{Description}
\begin{Usage}
\begin{verbatim}test2Interact(iMat, tMat, interactome)\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{iMat}] Genetic interaction matrix. Each entry has value 0 or 1,
representing positive or negative interaction of corresponding pairs
of row and column, respectively.
\item[\code{tMat}] Adjacency matrix of tested object. Each entry has value 0 or 1,
representing the fact that the corresponding pairs
of row and column have been tested for interaction or not.
\item[\code{interactome}] Adjacency matrix where  row are gene names and
columns are cellular organizational units names. Each entry has
value 0 or 1, for absence or presence of a gene in the complex.
\end{ldescription}
\end{Arguments}
\begin{Value}
the return value is a data.frame with 6 columns.

\begin{ldescription}
\item[\code{unit1, unit2}] cellular organizational units tested and
interacting
\item[\code{tested}] Number of interactions tested between unit1 and unit2
\item[\code{interact}] Number of interactions found between unit1 and unit2
\item[\code{sizeC1, sizeC2}] Number of genes in  unit1 and unit2
\end{ldescription}
\end{Value}
\begin{Author}\relax
N. LeMeur
\end{Author}
\begin{Examples}
\begin{ExampleCode}
set.seed(123)
##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]))

## Create cellular organizational units interaction matrix
gInt <- sample(c(1:8), 25, TRUE)
gInt  <- matrix(gInt, nrow=5, ncol=5, dimnames=list(LETTERS[1:5],LETTERS[1:5]))

## All interactome tested
gTest <- matrix(sample(c(0:3), 25, TRUE), nrow=5, ncol=5)
gTested <- gInt+gTest

val <- test2Interact(iMat=gInt, tMat=gTested, interactome=interactome)
\end{ExampleCode}
\end{Examples}

