separateXMLDataByExpt: Convert a vector of PSI-MI 2.5 XML files into graph objects...
In alyst/RpsiXML: R interface to PSI-MI 2.5 files

Description Usage Arguments Value Author(s) See Also Examples

The function 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.

1	separateXMLDataByExpt(xmlFiles, psimi25source, type = "direct", directed = TRUE, abstract = FALSE,...)

`xmlFiles`	Single file name or a vector of PSI-MI 2.5 XML file names or URLs.
`type`	A character. Currently the user can specify to cull either "direct" interactions or "indirect" interactions.
`psimi25source`	Source of the PSI-MI 2.5 XML file, see `psimi25Source-class`
`directed`	Logical, whehter the returned graph object should be directed or undirected.
`abstract`	Logical; if TRUE, the abstract information will be appended to the graph object.
`...`	Other parameters passed to `parsePsimi25Interaction`, for example `verbose=TRUE`

A list of psimi25Graph-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.

Jitao David Zhang, Tony Chiang

psimi25Source-class, psimi25Graph-class, psimi25Hypergraph-class

xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")

intactxml <- file.path(xmlDir, "intact_2008_test.xml")
intactGraph <- separateXMLDataByExpt(intactxml, INTACT.PSIMI25, type="indirect")