\HeaderA{complexStatus}{Complex Status}{complexStatus}
\keyword{data}{complexStatus}
\keyword{manip}{complexStatus}
\begin{Description}\relax
Categorize the complex whether or not a complex is composed of a
significant number of genes involved in a particular
phenotype than expected by chance.
\end{Description}
\begin{Usage}
\begin{verbatim}
complexStatus(data, phenotype, interactome, threshold=0.05)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{data}] Output from CoHyperG test
\item[\code{phenotype}] List of gene names inducing an observed phenotype,
e.g., list of essential gene names (see package \emph{SLGI})
\item[\code{interactome}] A binary matrix composed of genes (rows) and biological
complexes (columns) (see package \emph{ScISI})
\item[\code{threshold}] pvalue threshold (default 0.05)
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
We form four distinct categories from A to D to characterize how a
complex might be involved in a particular phenotype (according to
the number of genes it contains and that are involved in a particular
phenotype - see also \LinkA{CoHyperG}{CoHyperG} function)
\end{Details}
\begin{Value}
The returned value is a list with components:
\begin{ldescription}
\item[\code{A}] "interesting" complexes, complexes with a significant number of interesting
genes, i.e., genes that participate to a particular phenotype (at a given p-values threshold)
\item[\code{B}] complexes with a NON significant number of interesting genes
BUT that  SHARE genes with complexes from the A status
\item[\code{C}] complexes with a NON significant number of interesting genes AND
that DON'T SHARE interesting genes with complexes from cat A
\item[\code{D}] complexes WITHOUT interesting genes, i.e. the one involved in
the studied phenotype
\end{ldescription}
\end{Value}
\begin{Author}\relax
N. LeMeur
\end{Author}
\begin{Examples}
\begin{ExampleCode}
data(ScISI)
data(essglist)
essential <- names(essglist)

CoparamsESS <- new("CoHyperGParams",
                   geneIds=essential, 
                   universeGeneIds=rownames(ScISI),
                   annotation="org.Sc.sgd.db",
                   categoryName="ScISI",
                   pvalueCutoff=0.01,
                   testDirection="over")

sign<- hyperGTest(CoparamsESS)
test05 <-complexStatus(data=sign, phenotype=essential,
interactome=ScISI, threshold=0.05)
\end{ExampleCode}
\end{Examples}

