\HeaderA{calcInOutDegStats}{This function calculates the various degree statistic for a
Protein-Protein Interaction (PPI) Graph}{calcInOutDegStats}
\keyword{datagen}{calcInOutDegStats}
\begin{Description}\relax
This function takes a graphNEL argument and calculates several degree
statistics for which further analysis can be made.
\end{Description}
\begin{Usage}
\begin{verbatim}
calcInOutDegStats(graphObj, homodimer=FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{graphObj}] The argument \code{graphObj} is an instance of the 
class graphNEL.
\item[\code{homodimer}] A logical. If FALSE, the function removes all
homodimer relationships. It retains them otherwise.
\end{ldescription}
\end{Arguments}
\begin{Value}
The return value is a list of various degree statistics of the PPI directed
graph:
\begin{ldescription}
\item[\code{inDegree}] A named numeric vector. The names corresponds to the particular
yeast Open Reading Frame (ORF), and each entry details how many edges flow towards
that node, i.e. how many times each node was detected as a prey.
\item[\code{outDegree}] A named numeric vector. The names corresponds to the particular
yeast Open Reading Frame (ORF), and each entry details how many edges flow out from
that node, i.e. how many prey was detected by each node as a bait.
\item[\code{inDegreeMinusOutDegree}] A named numeric vector. This entry is the inDegree
minus the outDegree entries, or the signed difference for each node as a prey to 
each node as a bait.
\item[\code{outDegreeMinusInDegree}] A named numeric vector. This entry is the outDegree
minus the inDegree entries, or the signed difference for each node as a bait to 
each node as a prey.
\item[\code{recipInDegree}] A named numeric vector. Again the names represents the ORFs,
while each entry corresponds to how many times each node was found as a prey in a 
reciprocated interaction.
\item[\code{recipOutDegree}] A named numeric vector. Again the names represents the ORFs,
while each entry corresponds to how many times each node was found as a bait in a 
reciprocated interaction.
\item[\code{totalRecipDegree}] A numeric. For the PPI graph given, this argument gives the
total number of reciprocated interactions found.
\item[\code{unrecipInDegree}] A named numeric vector. The names corresponds ORF and 
each entry details how many edges flow towards each node modulo the reciprocated 
interactions, i.e. for each node $p$, how many baits $b$ detected $p$ as a prey with 
the condition that $p$ never detects $b$ as a prey.
\item[\code{unrecipOutDegree}] A named numeric vector. The names corresponds ORF and 
each entry details how many edges flow out from each node modulo the reciprocated 
interactions, i.e. for each node $b$, how many prey $p$ does $b$ detect with the 
condition that $b$ is never detected by $p$.
\item[\code{totalUnrecipDegree}] A numeric. The total number of unreciprocated interactions
for the PPI graph given.
\end{ldescription}

...
\end{Value}
\begin{Author}\relax
T Chiang
\end{Author}
\begin{Examples}
\begin{ExampleCode}
        library(ppiData)
        degStat <- calcInOutDegStats(Cagney2001BPGraph)
        degStat$recipOutDeg
\end{ExampleCode}
\end{Examples}

