psimi25XML2Graph: Convert a vector of PSI-MI 2.5 XML files into graph objects

Description Usage Arguments Value Author(s) See Also Examples

View source: R/psi25parser.R

Description

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. psimi25XML2Graph is a wrapper for interactionEntry2graph and complexEntry2graph, which transform interactionEntry list and complexEntry list into graphs respectively.

Usage

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psimi25XML2Graph(psimi25files, psimi25source, type = "interaction",
directed = TRUE, ...)

Arguments

psimi25files

Single file name or a vector of PSI-MI 2.5 XML file names or URLs. In case of splitted data the latter form is preferred. Different datasets or datasets from different sources should not be put into the same vector.

psimi25source

Source of the PSI-MI 2.5 XML file, see psimi25Source-class

type

A character string which is either "interaction" or "complex". As the value suggests, use "interaction" if the XML file contains experimental physical data, and "complex" if the file contains curated protein complex membership data.

directed

Logical, whehter the returned graph object should be directed or undirected

...

Other parameters passed to parsePsimi25Interaction

Value

If type is "interaction", then a resulting psimi25Graph object is genertated on the aggregation of the XML files. Otherwise if type is "complex,", a resulting psimi25HyperGraph object is generated on the aggregate of the XML files.

Author(s)

Jitao David Zhang, Tony Chiang

See Also

psimi25Source-class, psimi25Graph-class, psimi25Hypergraph-class

Examples

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

intactxml <- file.path(xmlDir, "intact_2008_test.xml")
intactGraph <- psimi25XML2Graph(intactxml, INTACT.PSIMI25, type="interaction")

intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml")
intactComplexGraph <- psimi25XML2Graph(intactComplexxml, INTACT.PSIMI25, type="complex")

alyst/RpsiXML documentation built on July 10, 2017, 11:46 p.m.