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RpsiXML (version 2.8.0)

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

2.8.0

License

LGPL-3

Maintainer

Jitao David Zhang

Last Published

February 15th, 2017

Functions in RpsiXML (2.8.0)

complexName

Accessor functions for complex
availableXrefs-methods

Methods for function availableXrefs
BIOGRID.PSIMI25

Supported PSI-MI 2.5 XML data sources
bait

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

xmlEventParse handlers for PSI-MI XML documents
graphConverter

maps one type of grap onto another
availableXrefs

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

Extract complexes from psimi25ComplexEntry
getAbstractByPMID

A function to obtain the abstract information via a Pubmed ID
buildPCHypergraph

Build protein complex hypergraph from PSI-MI 2.5 files
interactors

Get information of interactors of the given object
list2Matrix

Converts list into matrix
null2na

Turns null or NA into character "NA"
interactorInfo

Interactor info in a matrix
interactions

List interactions in the given psimi25InteractionEntry object
interactorInfo-methods

Methods for Function interactorInfo in Package `RpsiXML'
numInteractions-methods

Get interaction number of the given object
interactionType

Type of the interaction
psimi25Attribute-class

Class "psimi25Attribute"
parsePsimi25Interaction

Parsing PSI-MI 2.5 XML documents into interactions
psimi25Experiment-class

Class "psimi25Experiment"
psimi25Graph-class

Class "psimi25Graph" ~~~
psimi25Interactor-class

A class representing interactor from PSI-MI 2.5 XML files
psimi25Source-class

Class "psimi25Source"
psimi25InteractionEntry-class

Class "psimi25InteractionEntry"
psimi25Interaction-class

Class "psimi25Interaction"
psimi25Complex-class

Class "psimi25Complex"
psimi25Hypergraph-class

Class "psimi25Hypergraph"
psimi25ComplexEntry-class

Class "psimi25ComplexEntry"
psimi25Hypergraph2GraphNEL

Convert psimi25Hypergraph to graphNEL
uniprot-methods

Methods for Function uniprot in Package `RpsiXML'
uniprot

The UniProt Identifier in the PSI-MI 2.5 XML file
validatePSIMI25

Validating PSI-MI 2.5 file with MIF25 XML schema
sourceId-methods

Extract or set source database name or ID in the source database
taxId-methods

Get or Set the NCBI Taxonomy ID or Organism Name
translateID

Finds identifiers of a given object
translateID-methods

Translate interactors into other identifiers
separateXMLDataByExpt

Convert a vector of PSI-MI 2.5 XML files into graph objects based on pubmedID
psimi25XML2Graph

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