R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 39 found.
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validatePSIMI25 (Package: RpsiXML) : Validating PSI-MI 2.5 file with MIF25 XML schema

The function validates given PSI-MI 2.5 file with MIF25 XML schema provided by the Molecular Interactions Workgroup of HUPO Proteomics Standards Initiative

● Data Source: BioConductor
● Keywords: models
● Alias: validatePSIMI25
● 0 images

BIOGRID.PSIMI25 (Package: RpsiXML) : Supported PSI-MI 2.5 XML data sources

Objects representing supported PSI-MI 2.5 XML data sources. They are implicitly used in interaction and/or complex parsers. The supporting list will grow as soon as there are new PSI-MI 2.5 compatible data sources available.

● Data Source: BioConductor
● Keywords: models
● Alias: BIOGRID.PSIMI25, CORUM.PSIMI25, DIP.PSIMI25, HPRD.PSIMI25, INTACT.PSIMI25, MATRIXDB.PSIMI25, MINT.PSIMI25, MIPS.PSIMI25, MPACT.PSIMI25
● 0 images

availableXrefs-methods (Package: RpsiXML) : Methods for function availableXrefs

Methods for function availableXrefs. See availableXrefs for more details

● Data Source: BioConductor
● Keywords: methods, models
● Alias: availableXrefs,list-method, availableXrefs,psimi25InteractionEntry-method, availableXrefs,psimi25Interactor-method, availableXrefs-methods
● 0 images

availableXrefs (Package: RpsiXML) : Get cross reference(s) of interactors from PSI-MI 2.5 files

PSI-MI 2.5 data exchange format encourages data providers to encode cross referenes of the interactors into the file, which prove valuable for annotating the data. These functions help finding out the available cross references of interactors.

● Data Source: BioConductor
● Keywords: models
● Alias: availableXrefs, xref
● 0 images

bait (Package: RpsiXML) : Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type,

The functions return bait/prey UniProt identifier of the given psimi25Interaction object.

● Data Source: BioConductor
● Keywords: models
● Alias: bait, confidenceValue, inhibitor, neutralComponent, participant, prey, pubmedID
● 0 images

buildPCHypergraph (Package: RpsiXML) : Build protein complex hypergraph from PSI-MI 2.5 files

The protein complexes can be represented by hypergraph models, with proteins as nodes and complexes as hypergraphs. This function builds protein complex hypergraph from one or more PSI-MI 2.5 files (complex mode), with the option to split the dataset by organism name or taxonomy ID of the complexes.

● Data Source: BioConductor
● Keywords:
● Alias: buildPCHypergraph
● 0 images

complexName (Package: RpsiXML) : Accessor functions for complex

These functions are used to extract useful information of complex in the form of psimi25Complex-class object.

● Data Source: BioConductor
● Keywords: models
● Alias: attributesList, complexName, members
● 0 images

complexes (Package: RpsiXML) : Extract complexes from psimi25ComplexEntry

Extract complexes from an object of psimi25ComplexEntry-class

● Data Source: BioConductor
● Keywords: models
● Alias: complexes
● 0 images

eListHandler (Package: RpsiXML) : xmlEventParse handlers for PSI-MI XML documents

xmlEventParse handlers for PSI-MI XML documents

● Data Source: BioConductor
● Keywords: models
● Alias: eListHandler, iListHandler
● 0 images

getAbstractByPMID (Package: RpsiXML) : A function to obtain the abstract information via a Pubmed ID

This function takes a character vector of pubmed IDs and returns a list of pubMedAbst objects indexed by each ID.

● Data Source: BioConductor
● Keywords: models
● Alias: getAbstractByPMID
● 0 images