\HeaderA{getTestedPairs}{Find interacting and  non-interacting tested pairs from an genetic interaction matrix.}{getTestedPairs}
\keyword{methods}{getTestedPairs}
\begin{Description}\relax
\code{getTestedPairs} find all the pairs from an
interaction matrix and a list of tested genes.
\end{Description}
\begin{Usage}
\begin{verbatim}getTestedPairs(iMat, respV)\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, respectively.
\item[\code{respV}] Character vector of all gene names that were tested
(found to interact or not) 
\end{ldescription}
\end{Arguments}
\begin{Value}
A data.frame with 4 columns:
\begin{ldescription}
\item[\code{query}] gene names of the query genes
\item[\code{array}] gene names og the tested genes (e.g., array genes)
\item[\code{interact}] numeric vector of the number of observed interactions
(0: no interaction; 1: one interaction; 2: two interactions when the
query genes were also on the array)
\item[\code{recip}] logical to indicate whether the reported genes were both
query and array genes (TRUE: both genes were query and array genes)
\end{ldescription}
.
\end{Value}
\begin{Author}\relax
N. LeMeur
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{getSharedDomains}{getSharedDomains}} \code{\LinkA{getUniquePairs}{getUniquePairs}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
intM <- c(0,1,0,0,1,1,0,0,1,0,0,1,1,0,1,0)
dim(intM) <- c(4,4)
dimnames(intM) <- list(c("p1","p2","p3","p4"),c("p1","p3","p5","p7") )
respV <- c("p6","p8")
intM
getTestedPairs(intM,respV)
\end{ExampleCode}
\end{Examples}

