\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. In general,
the entry of this function should be that data from one experiment 
(this data might be divided into several XML files). If the XML file
contains data that should not be combined into one single graph, 
this function should not be called; the function 
\code{\LinkA{separateXMLDataByExpt}{separateXMLDataByExpt}} should be used instead.
\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
Rintact: enabling computational analysis of molecular interaction data
from the IntAct repository - Tony Chiang; Nianhua Li; Sandra Orchard; Samuel 
Kerrien; Henning Hermjakob; Robert Gentleman; Wolfgang Huber
Bioinformatics 2007; doi: 10.1093/bioinformatics/btm518.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{interactionEntry-class}{interactionEntry.Rdash.class}}, \code{\LinkA{complexEntry-class}{complexEntry.Rdash.class}},        
\code{\LinkA{separateXMLDataByExpt}{separateXMLDataByExpt}}
\end{SeeAlso}

