\HeaderA{sharedInt}{List shared genetic interactions between genes}{sharedInt}
\keyword{data}{sharedInt}
\keyword{manip}{sharedInt}
\begin{Description}\relax
List shared interactions and cellular organizational units names between genes.
\end{Description}
\begin{Usage}
\begin{verbatim}sharedInt(pairL, interactome, threshold=0)\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{pairL}] Dataframe with 3 columns. The first columns are the pair
of genes tested i.e., the query and array genes. The third columns
in a logical: TRUE when the 2 genes genetically interact and FALSE
when they do not.(see \code{AtongPair} dataset as example)
\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.
\item[\code{threshold}] Numeric. Indicate the minimum number of interactions that 2
genes must share
\end{ldescription}
\end{Arguments}
\begin{Value}
The return value is a list. Each element of the list has for name 2
genes that genetically interact. Each element of the list corresponds to the
list of cellular organizational units where the interacting genes are
found (independently or together).
\end{Value}
\begin{Author}\relax
N. LeMeur
\end{Author}
\begin{Examples}
\begin{ExampleCode}
## Synthetic genetic interactions 
dat <- data.frame("query" = LETTERS[1:5], "array" = LETTERS[2:6], "interact" = as.logical(sample(c(TRUE, FALSE), 5, TRUE)))
## interactome
interA <- matrix(sample(c(0, 1), 30,TRUE), nrow=6, ncol=5,dimnames = list(LETTERS[1:6], letters[1:5]))

sharedInt(dat, interA, threshold=1)
\end{ExampleCode}
\end{Examples}

