\HeaderA{intactXML2Graph}{A function that takes a vector of IntAct XML file names
and converts them to graph objects.}{intactXML2Graph}
\keyword{models}{intactXML2Graph}
\begin{Description}\relax
The \code{intactXML2Graph} takes in a vector of related XML files
and generates a graph object based on the type of XML file.
\end{Description}
\begin{Usage}
\begin{verbatim}
intactXML2Graph(intactFiles, type="interaction", directed=TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{intactFiles}] A vector of IntAct XML file names. If the data 
of a single experiment has been split into multiple XML files 
(e.g. Ewing et al 2007), then each entry of the vector should contain
one of these XML files. NB - different datasets should not be 
put into the same vector.
\item[\code{type}] A character string which is either "interaction" if the
XML file contains experimental physical data or "complex" if the 
XML file contains curated protein complex membership data.
\item[\code{directed}] A logical. User defined parameter so that the return
value with either be a directed or undirected graph object.
\end{ldescription}
\end{Arguments}
\begin{Value}
If type = "interaction," then a resulting intactGraph object is genertated on the
aggregate of the XML files. If type = "complex," then a resulting intactHyperGraph
object is generated on the aggregate of the XML files.
\end{Value}
\begin{Author}\relax
T Chiang
\end{Author}
\begin{References}\relax
The IntAct Database \url{http://www.ebi.ac.uk/intact/site/contents/downloads.jsf}.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{interactionEntry-class}{interactionEntry.Rdash.class}}, \code{\LinkA{complexEntry-class}{complexEntry.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# parse complex data
\end{ExampleCode}
\end{Examples}

