\HeaderA{densityEstimate}{Observed versus Expected Ratios}{densityEstimate}
\keyword{data}{densityEstimate}
\keyword{manip}{densityEstimate}
\begin{Description}\relax
Function to calculate the ratio of genes that characterize a phenotype
(observed) among the genes that characterize a biological complex
versus the ratio of a set of randomly sampled genes (expected) among
the genes that characterize a biological complex.
\end{Description}
\begin{Usage}
\begin{verbatim}
densityEstimate(genename,interactome,perm)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{genename}] Character vector of the gene names that characterize
a specific phenotype.
\item[\code{interactome}] Contingency matrix of genes (rows) and biological
complexes (columns) (see package \emph{ScISI}) 
\item[\code{perm}] Numeric vector indicating the number of simulations to
run to compute the expected ratios.
\end{ldescription}
\end{Arguments}
\begin{Value}
List of observed and simulated ratios.
\end{Value}
\begin{Author}\relax
N. LeMeur
\end{Author}
\begin{Examples}
\begin{ExampleCode}
 data(ScISI)
 data(essglist)
 essential <- names(essglist)
 ScISI <- as.matrix(ScISI)
  ratio<- densityEstimate(genename=essential,interactome=ScISI,perm=50)
\end{ExampleCode}
\end{Examples}

