\HeaderA{estimateCCMErrorRates}{Estimate false positive and false negative error probabilities}{estimateCCMErrorRates}
\keyword{manip}{estimateCCMErrorRates}
\begin{Description}\relax
Estimate false positive and false negative error probabilities
for complex comembership edges using a protein complex interactome
gold standard
\end{Description}
\begin{Usage}
\begin{verbatim}
estimateCCMErrorRates(m,GS,filterSystematic=TRUE,       
         obsPropThresh=1,SystematicpThresh=.01)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{m}] The bait to prey data adjacency matrix. Baits index the rows and prey index
the columns.
\item[\code{GS}] A gold standard protein complex interaction incidence matrix. Proteins index
the rows and protein complexes index the columns. 
\item[\code{filterSystematic}] A logical. If TRUE, all baits with with highly uneven
directed degree will be filtered out of the data.
\item[\code{obsPropThresh}] A numeric between 0 and 1. The proportion of tested proteins found
within a protein complex needed to keep that protein complex within
the gold standard set.
\item[\code{SystematicpThresh}] A numeric between 0 and 1. The p-value threshold by which
systematic errors are filtered.
\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 list:


\begin{ldescription}
\item[\code{globalpTP}] A numeric between 0 and 1.  Estimate of pTP.
\item[\code{globalpTPSE}] A numeric.  Estimate of standard error of globalpTP estimate.
\item[\code{globalpFP}] A numeric between 0 and 1.  Estimate of pFP.
\item[\code{pTP95CI}] A vector of length 2.  95 percent confidence interval upper and lower
bounds for globalpTP estimate.
\item[\code{pFP95CI}] A vector of length 2.  95 percent confidence interval upper and lower
bounds for globalpFP estimate.
\item[\code{nEligComplexes}] A numeric.  Number of complexes from GS that met
obsPropThresh criteria.
\item[\code{nEligBaits}] A numeric. Total number of eligible baits in GS set.
\item[\code{nEligEdges}] A numeric.  Total number of eligible edges in GS set.
\item[\code{nBaitsInComplexes}] A vector.  Number of baits in each eligible complex.
\item[\code{complexSizes}] A vector. Size of each complex in GS set.
\end{ldescription}
\end{Value}
\begin{Author}\relax
T. Chiang and D. Scholtens
\end{Author}
\begin{References}\relax
Scholtens D, Chiang T, Huber W, Gentleman R.  Estimating node
degree in bait-prey graphs. \emph{Bioinformatics}.  To appear.
\end{References}
\begin{Examples}
\begin{ExampleCode}
data(Ho2002BPGraph)
data(ScISIC)
Ho2002mat = as(Ho2002BPGraph,"matrix")
estimateCCMErrorRates(Ho2002mat,ScISIC)$globalpTP
\end{ExampleCode}
\end{Examples}

