separateXMLDataByExpt {RpsiXML} | R Documentation |
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.
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)