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RpsiXML (version 2.14.0)

R interface to PSI-MI 2.5 files

Description

Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously.

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Version

Version

2.14.0

License

LGPL-3

Maintainer

Jitao David Zhang

Last Published

February 15th, 2017

Functions in RpsiXML (2.14.0)

buildPCHypergraph

Build protein complex hypergraph from PSI-MI 2.5 files

Turns null or NA into character "NA"

Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type, or neutral component information from an object of psimi25Interaction-class

psimi25InteractionEntry-class

Class "psimi25InteractionEntry"

Get cross reference(s) of interactors from PSI-MI 2.5 files

psimi25Experiment-class

Class "psimi25Experiment"

psimi25Interactor-class

A class representing interactor from PSI-MI 2.5 XML files

numInteractions-methods

Get interaction number of the given object

Converts list into matrix

psimi25Graph-class

Class "psimi25Graph" ~~~

psimi25ComplexEntry-class

Class "psimi25ComplexEntry"

psimi25Hypergraph-class

Class "psimi25Hypergraph"

Get information of interactors of the given object

psimi25XML2Graph

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

sourceId-methods

Extract or set source database name or ID in the source database

Extract complexes from psimi25ComplexEntry

Accessor functions for complex

interactionType

Type of the interaction

maps one type of grap onto another

The UniProt Identifier in the PSI-MI 2.5 XML file

psimi25Interaction-class

Class "psimi25Interaction"

interactorInfo-methods

Methods for Function interactorInfo in Package `RpsiXML'

psimi25Hypergraph2GraphNEL

Convert psimi25Hypergraph to graphNEL

Finds identifiers of a given object

psimi25Complex-class

Class "psimi25Complex"

validatePSIMI25

Validating PSI-MI 2.5 file with MIF25 XML schema

getAbstractByPMID

A function to obtain the abstract information via a Pubmed ID

translateID-methods

Translate interactors into other identifiers

separateXMLDataByExpt

Convert a vector of PSI-MI 2.5 XML files into graph objects based on pubmedID

psimi25Attribute-class

Class "psimi25Attribute"

BIOGRID.PSIMI25

Supported PSI-MI 2.5 XML data sources

uniprot-methods

Methods for Function uniprot in Package `RpsiXML'

availableXrefs-methods

Methods for function availableXrefs

List interactions in the given psimi25InteractionEntry object

parsePsimi25Interaction

Parsing PSI-MI 2.5 XML documents into interactions

Interactor info in a matrix

xmlEventParse handlers for PSI-MI XML documents

psimi25Source-class

Class "psimi25Source"

Get or Set the NCBI Taxonomy ID or Organism Name