psimi25Hypergraph-class: Class "psimi25Hypergraph"

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

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 <[email protected]> , Jitao David Zhang <[email protected]>

See Also

psimi25XML2Graph,S4classpsimi25Graph-class

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")
intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml")
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]]

alyst/RpsiXML documentation built on July 10, 2017, 11:46 p.m.