\HeaderA{estimatePPIErrorRates}{Estimate false positive and false negative error probabilities
for direct protein interactions}{estimatePPIErrorRates}
\keyword{manip}{estimatePPIErrorRates}
\begin{Description}\relax
Estimate false positive and false negative error probabilities
for direct protein interactions using a protein interaction graph
gold standard
\end{Description}
\begin{Usage}
\begin{verbatim}
estimatePPIErrorRates(matList,GSPos=NULL,GSNeg=NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{matList}] A named list of list. The names corresponds to a
particular publication. Each element of the top list is a list of
two matrices:
1. The adjacency matrix of the positive interaction
datapoints.
2. The adjacency matrix of the tested interaction datapoints.
The dimension names of these two matrices should be identical (an
error will be thrown if this is not the case) where the rows are
indexed by the bait proteins and the columns are indexed by the
prey. The adjacency matrices are 0,1 matrices where an 1 entry
signifies either a positive interaction relationship or a positive
tested relationship. A 0 entry is then well defined.
\item[\code{GSPos}] A positive gold standard protein interaction graph given by its
adjacency matrix. The dimension names of this matrix must be the same
identifying system used for the dimension names for the matrices found
within the matList parameter. An entry of one in this matrix indicates
a positive interaction while an entry of zero is inconclusive.
\item[\code{GSNeg}] A negative gold standard protein interaction graph given by its
adjacency matrix. The dimension names of this matrix must be the same
identifying system used for the dimension names for the matrices found
within the matList parameter. An entry of one in this matrix indicates
a negative interaction while an entry of zero is inconclusive.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The model is described in the manuscript
\emph{Estimating node degree in bait-prey graphs.}
by D. Scholtens et al.
\end{Details}
\begin{Value}
A matrix.

The return value is an kx2 matrix where k is the length of
matList. The first colum returns the estimated false positive error
rates and the second column returns the estimated false negative error
rates.
\end{Value}
\begin{Author}\relax
T. Chiang and L. Wang
\end{Author}
\begin{References}\relax
Scholtens D, Chiang T, Huber W, Gentleman R.  Estimating node
degree in bait-prey graphs. \emph{Bioinformatics}.
\end{References}
\begin{Examples}
\begin{ExampleCode}
load(system.file("extdata", "intacty2hppMatrix.rda", package="ppiStats"))
load(system.file("extdata", "PPIpos", package="ppiStats"))
x = intacty2hppMatrix[c("EBI-389903","EBI-783101")]
estimatePPIErrorRates(x, GSPos=PPIpos)
\end{ExampleCode}
\end{Examples}

