\HeaderA{separateXMLDataByExpt}{Convert a vector of PSI-MI 2.5 XML files into graph objects based on pubmedID}{separateXMLDataByExpt}
\keyword{models}{separateXMLDataByExpt}
\begin{Description}\relax
The function \code{psimi25XML2Graph} take a vector of XML 2.5 files
from te same data source and generates a graph object based on the
type of the files.
\end{Description}
\begin{Usage}
\begin{verbatim}
separateXMLDataByExpt(xmlFiles, psimi25source, type = "direct", directed = TRUE, abstract = FALSE,...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{xmlFiles}] Single file name or a vector of PSI-MI 2.5 XML file names or
URLs.
\item[\code{type}] A character. Currently the user can specify to cull either "direct"
interactions or "indirect" interactions.
\item[\code{psimi25source}] Source of the PSI-MI 2.5 XML file, see \code{\LinkA{psimi25Source-class}{psimi25Source.Rdash.class}}
\item[\code{directed}] Logical, whehter the returned graph object should be
directed or undirected.
\item[\code{abstract}] Logical; if TRUE, the abstract information will be
appended to the graph object.
\item[\code{...}] Other parameters passed to
\code{\LinkA{parsePsimi25Interaction}{parsePsimi25Interaction}}, for example \code{verbose=TRUE}
\end{ldescription}
\end{Arguments}
\begin{Value}
A list of \code{\LinkA{psimi25Graph-class}{psimi25Graph.Rdash.class}} are generated indexed by the pubmedID of
each bait-prey interaction. WARNING - the abstract information is obtained using the 
pubmed and buildPubMedAbst functions from the 
annotate package which warns the user that NCBI may block access to
their site. The default is to not obtain the abstract for this reason.
\end{Value}
\begin{Author}\relax
Jitao David Zhang, Tony Chiang
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{psimi25Source-class}{psimi25Source.Rdash.class}},
\code{\LinkA{psimi25Graph-class}{psimi25Graph.Rdash.class}},
\code{\LinkA{psimi25Hypergraph-class}{psimi25Hypergraph.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")

intactxml <- file.path(xmlDir, "intact_2008_test.xml")
intactGraph <- separateXMLDataByExpt(intactxml, INTACT.PSIMI25)
\end{ExampleCode}
\end{Examples}

