psimi25Hypergraph-class {RpsiXML} | R Documentation

## Class "psimi25Hypergraph"

### Description

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

### Objects from the Class

Objects can be created by calls of the form `psimi25XML2Graph`

### Slots

`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.

### Extends

Class `Hypergraph`, directly

### Methods

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

### Author(s)

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

### See Also

`psimi25XML2Graph`,`S4classpsimi25Graph-class`

### Examples

    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]]

[Package RpsiXML version 2.36.0 Index]