\HeaderA{simLL}{Functions to compute similarities between GO graphs and also
between Entrez Gene IDs based on their induced GO graphs.}{simLL}
\aliasA{simLP}{simLL}{simLP}
\aliasA{simUI}{simLL}{simUI}
\keyword{manip}{simLL}
\begin{Description}\relax
Both \code{simUI} and \code{simLP} compute a similarity measure
between two GO graphs. For \code{simLL}, first the induced GO graph
for each of its arguments is found and then these are passed to one
of \code{simUI} or \code{simLP}.
\end{Description}
\begin{Usage}
\begin{verbatim}
simLL(ll1, ll2, Ontology = "MF", measure = "LP", dropCodes = NULL)
simUI(g1, g2)
simLP(g1, g2)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{ll1}] A Entrez Gene ID as a character vector. 
\item[\code{ll2}] A Entrez Gene ID as a character vector.
\item[\code{Ontology}] Which ontology to use ("MF", "BP", "CC"). 
\item[\code{measure}] Which measure to use ("LP", "UI"). 
\item[\code{dropCodes}] A set of evidence codes to be ignored in
constructing the induced GO graphs. 
\item[\code{g1}] An instance of the \code{graph} class.
\item[\code{g2}] An instance of the \code{graph} class.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
For each of \code{ll1} and \code{ll2} the set of most specific GO
terms within the ontology specified (\code{Ontology}) that are not
based on any excluded evidence code (\code{dropCodes}) are
found. Then the induced GO graphs are computed.

Finally these graphs are passed to one of \code{simUI}, (union
intersection), or \code{simLP} (longest path). For \code{simUI} the
distance is the size of the intersection of the node sets divided by
the size of the union of the node sets. Large values indicate more
similarity. These similarities are between 0 and 1.

For \code{simLP} the length of the longest path in the intersection
graph of the two supplied graph. Again, large values indicate more
similarity. Similarities are between 0 and the maximum leaf depth of
the graph for the specified ontology.
\end{Details}
\begin{Value}
A list with:
\begin{ldescription}
\item[\code{sim }] The numeric similarity measure.
\item[\code{measure}] Which measure was used.
\item[\code{g1}] The graph induced by \code{ll1}.
\item[\code{g2}] The graph induced by \code{ll2}.
\end{ldescription}


If one of the supplied Gene IDs does not have any GO terms associated
with it, in the selected ontology and with the selected evidence codes
then \code{NA} is returned.
\end{Value}
\begin{Author}\relax
R. Gentleman
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{makeGOGraph}{makeGOGraph}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  aa = simLL("111", "112")
  bb = simLL("9184", "3547", "BP")
\end{ExampleCode}
\end{Examples}

