psimi25Hypergraph-class: Class "psimi25Hypergraph"
In Accio/RpsiXML: R interface to PSI-MI 2.5 files

Description Objects from the Class Slots Extends Methods Author(s) See Also Examples

Class to present PSI-MI 2.5 XML data as hypergraph. Proteins are projected as hypergraph nodes and complex composition as hyperedges.

Objects can be created by calls of the form psimi25XML2Graph

interactors:: Object of class "matrix", Object of class "matrix", interactor information in a matrix, Each row represents one interactor. Source IDs are used as row names. Each column represents one annotation. Annotations include: UniProt ID, short label, organism name, and NCBI taxonomy ID. Only those interactors which are the nodes of the psimi25Graph is given.

Class Hypergraph, directly

initialize: signature(.Object = "psimi25Hypergraph")
show: signature(object = "psimi25Hypergraph"): show method,print complex and protein number
interactors: signature(object = "psimi25Hypergraph"): list of psimi25Interactor objects, providing full information of complex members
edgeLabel: signature(object = "psimi25Hypergraph"): returns complex names (as hyperedge label), as a character vector
hyperedgeNodes: signature(object = "Hypergraph"): returns a list of characters: names of the list are complex names and character vector in each list item are the members of that complex
complexes: signature(object = "psimi25Hypergraph"): a wrapper of hyperedgeNodes
translateSourceID: signature(r = "psimi25Hypergraph"): translate source ID into other IDs
numInteractors: signature(r = "psimi25Hypergraph"): returns the number of proteins
interactorInfo: signature(r = "psimi25Hypergraph"): returns a data frame containing essential information of the interactors
numEdges: signature(r = "psimi25Hypergraph"): returns the number of complexes
revInciMat: signature(r = "matrix"): returns the hypergraph built from the incidence matrix

Tony Chiang <tchiang@ebi.ac.uk> , Jitao David Zhang <jitao_david.zhang@roche.com>

psimi25XML2Graph,S4classpsimi25Graph-class

xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")
intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml.gz")
pc1 <- buildPCHypergraph(intactComplexxml, INTACT.PSIMI25)

## print number of proteins and complexes (edges)
numNodes(pc1)
## the same as numInteractors(pc1)
numEdges(pc1)

## print proteins (nodes)
nodes(pc1)[1:3]

## print complex names
edgeLabel(pc1)[1:3]

## print complexes (not so informative with 'hyperedges')
hyperedges(pc1)[1:3]
## better with 'complexes' or 'hyperedgeNodes'
complexes(pc1)[1:3]

## get interactor detailed information
interactors(pc1)[[1]]