\HeaderA{ppiInteract}{Test the association between AP-MS data and phenotype}{ppiInteract}
\keyword{data}{ppiInteract}
\keyword{manip}{ppiInteract}
\begin{Description}\relax
Test the association between AP-MS data and phenotype data via a graph
and permutation model.
\end{Description}
\begin{Usage}
\begin{verbatim}
ppiInteract(genename, expGraph, bait, prey, perm=10)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{genename}] Genes associated to a phenotype
\item[\code{expGraph}] A graphNEL object (a direct graph instance of class\code{graph}).
The nodes are the union of viable baits (VB) and viable
prey (VP) of the experiment (see package \emph{ScISI})
\item[\code{bait}] Proteins which was sampled as a bait in the binary
relationship
\item[\code{prey}] Proteins which was sampled as a prey in the binary
relationship
\item[\code{perm}] Number of permutation
\end{ldescription}
\end{Arguments}
\begin{Value}
The returned value is a list:
\begin{ldescription}
\item[\code{Observed}] Observed values
\item[\code{Expected}] Expected values after each permutation
\end{ldescription}
\end{Value}
\begin{Author}\relax
R. Gentleman and N. LeMeur
\end{Author}
\begin{SeeAlso}\relax
\emph{ScISI}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(ScISI)
data(essglist)
s1 <- ppiInteract(names(essglist), Gavin2002BPGraph, viableBaits[[8]],
       viablePrey[[8]], perm=10)
\end{ExampleCode}
\end{Examples}

