\HeaderA{getUniquePairs}{Find unique pairs from an genetic interaction matrix.}{getUniquePairs}
\keyword{methods}{getUniquePairs}
\begin{Description}\relax
\code{getUniquePairs} can find all the unique pairs from an
interaction matrix and supplementary array genes, or finds only the
unique pairs that shows positive interaction.
\end{Description}
\begin{Usage}
\begin{verbatim}getUniquePairs(iMat, respV = character(0), only = FALSE)\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)
\item[\code{only}] has default value \code{FALSE}, if \code{TRUE}, then only
reports the positively interacted pairs. 
\end{ldescription}
\end{Arguments}
\begin{Value}
A data.frame with two or three columns.  The first two columns are the
query gene name and the array gene name, respectively.  If \code{only}
is \code{TRUE}, the third column shows the interaction status.
\end{Value}
\begin{Author}\relax
Z. Jiang
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{getSharedDomains}{getSharedDomains}}
\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
getUniquePairs(intM,respV,only=FALSE)
getUniquePairs(intM,respV,only=TRUE)
getUniquePairs(intM,only=FALSE)
getUniquePairs(intM,only=TRUE)
\end{ExampleCode}
\end{Examples}

