\Header{distCGO}{Distances between GO graphs}
\alias{distDGGO}{distCGO}
\keyword{manip}{distCGO}
\begin{Description}\relax
These functions provide different ways of measuring the distance
between two GO graphs. See \code{oneGOGraph} for a description of how
these graphs are constructed.
\end{Description}
\begin{Usage}
\begin{verbatim}
distCGO(term1, term2, dataenv)
distDGGO(term1, term2, dataenv)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{term1}] The term used to construct the first graph. 
\item[\code{term2}] The term used to construct the second graph. 
\item[\code{dataenv}] The data used to construct both graphs. 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
A number of distances between induced GO graphs have been considered
in the literature. A basic idea behind these distances is to convey
some information about the relatedness of the terms (or possibly of
the genes annotated at those terms) using these distance measures.

For \code{distDGGO} the distance is the number of nodes in the
intersection of the two induced graphs divided by the number of nodes
in the union of the two graphs.

For \code{distCGO} the distance is not yet implemented.
\end{Details}
\begin{Value}
A numeric value indicating the distance between \code{term1} and
\code{term2}.
\end{Value}
\begin{Author}\relax
R. Gentleman
\end{Author}
\begin{References}\relax
(1) Cheng et al, Affymetrix. (2) B. Ding and R. Gentleman
\end{References}
\begin{SeeAlso}\relax
\code{\Link{oneGOGraph}}, \code{\Link{makeGOGraph}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
 distDGGO("GO:0005488", "GO:0030528", GOMFPARENTS)

 distDGGO("GO:0003700", "GO:0030528", GOMFPARENTS)

\end{ExampleCode}
\end{Examples}

