\HeaderA{idProteinType}{A function to determine viable baits, viable preys, or
homodimers within experimental data-sets.}{idProteinType}
\aliasA{idHomodimers}{idProteinType}{idHomodimers}
\aliasA{idViableProteins}{idProteinType}{idViableProteins}
\keyword{datagen}{idProteinType}
\begin{Description}\relax
These functions take a bait to prey directed graphNEL and returns
either a character vector of all proteins which participates in
homodimer relationships or a list of three character vectors: a vector
of viable baits, a vector of viable prey, and a vector of the viable
bait/prey.
\end{Description}
\begin{Usage}
\begin{verbatim}
idViableProteins(bpGraph, homomer=TRUE)
idHomodimers(bpGraph)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{bpGraph}] A directed graphNEL
\item[\code{homomer}] A logical. If True, homomer relationships will also be used to 
characterize proteins as viable baits, viable prey, and also as
viable bait/prey simultaneously. If False, those proteins whose
only intraction is a homomer relationship will not be 
characterized as viable in any context.
\end{ldescription}
\end{Arguments}
\begin{Value}
The return value for idHomodimers is a character vector of those
proteins which participates in homomer relationships.

The return value for idViableProteins is a list of two character
vectors:

\begin{ldescription}
\item[\code{VB}] A vector of baits that finds at least one prey in
the experimental graphNEL, i.e. the nodes with out-degree at greater
than 0. If homomer = FALSE, those proteins which participate in 
only homomer relationships will not be returned.
\item[\code{VP}] A vector of prey which is found by at least one bait in
the experimental graphNEL, i.e. the nodes with in-degree at greater
than 0. If homomer = FALSE, those proteins which participate in 
only homomer relationships will not be returned.
\item[\code{VBP}] A vector of proteins that are both viable baits and viable
prey in an experimental dataset as defined above. If 
homomer = FALSE, those proteins which participate in 
only homomer relationships will not be returned.
\end{ldescription}
\end{Value}
\begin{Author}\relax
T Chiang
\end{Author}
\begin{Examples}
\begin{ExampleCode}
library(ppiData)
idViableProteins(ItoCore2001BPGraph)
idHomodimers(ItoCore2001BPGraph)
\end{ExampleCode}
\end{Examples}

