\HeaderA{congruence}{Calculate congruence score between pairs of of genes sharing
pattern of synthetic genetic interactions
(Ye et al. (2005)).}{congruence}
\keyword{methods}{congruence}
\begin{Description}\relax
The \code{congruence} score represents the number of common synthetic genetic
interacting partners between two genes. The higher is the score
the more overlap there is between the synthetic genetic partners of
those genes.
\end{Description}
\begin{Usage}
\begin{verbatim}congruence(iMat, sharedInt, mode="query", universe, padjust=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{sharedInt}] numeric vector representing the number of common
genetic interactions between a pair
of query or target genes. See \code{getSharedInteraction}
for more details
\item[\code{mode}] character vector of value "query" or "target"
\item[\code{universe}] total number of genes tested
\item[\code{padjust}] adjust by the number of genes tested that show at least
one synthetic genetic interaction.
\end{ldescription}
\end{Arguments}
\begin{Value}
A numeric vector of the congruence score values.
\end{Value}
\begin{Author}\relax
N. LeMeur
\end{Author}
\begin{References}\relax
Ye P. et al. (2005). Gene function prediction from congruent
synthetic lethal interactions in yeast. Molecular Systems Biology 1:2005.0026.
\end{References}
\begin{SeeAlso}\relax
\code{getSharedInteraction}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
intM <- matrix(c(0,1,0,0,1,1,1,0,1,1,1,1,1,0,1,1),
                nrow=4, ncol=4, 
                dimnames=list(c("p1","p2","p3","p4"),
                  c("p1","p3","p5","p7")))
sharedInt <- getSharedInteraction(intM)
score <- congruence(intM, sharedInt, mode="query", universe=15, padjust=FALSE)
\end{ExampleCode}
\end{Examples}

