psi25interaction {Rintact}R Documentation

parser for PSI-MI 2.5 XML documents from EBI intact

Description

The PSI-MI 2.5 XML format is used by EBI IntAct database to record protein-protein interaction data and protein complex data. psi25interaction is the parser for interaction data and psi25complex is the parser for complex data.

Usage

psi25interaction(intactFile)
psi25complex(intactFile)

Arguments

intactFile character, file name or URL of the XML document

Value

psi25interaction returns a list of interactionEntry objects, each represents one entry in the XML document. psi25complex returns an complexEntry object, which represents the data from one XML document.

Author(s)

Nianhua Li

References

The IntAct Database http://www.ebi.ac.uk/intact/site/contents/downloads.jsf.

See Also

interactionEntry-class, complexEntry-class

Examples

# parse complex data
fn <- system.file("PSI25XML/complexSample.xml", package="Rintact")
complexData <- psi25complex(fn)
complexData

# parse interaction data
fn <- system.file("PSI25XML/interactionSample.xml", package="Rintact")
interactionData <- psi25interaction(fn)
interactionData

[Package Rintact version 1.4.0 Index]