psimi25Hypergraph-class {RpsiXML} | R Documentation |
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
:"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
signature(.Object = "psimi25Hypergraph")
signature(object = "psimi25Hypergraph")
: show
method,print complex and protein numbersignature(object = "psimi25Hypergraph")
:
list of psimi25Interactor
objects, providing full
information of complex memberssignature(object = "psimi25Hypergraph")
:
returns complex names (as hyperedge label), as a character vectorsignature(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 complexsignature(object = "psimi25Hypergraph")
:
a wrapper of hyperedgeNodes
signature(r = "psimi25Hypergraph")
:
translate source ID into other IDs signature(r = "psimi25Hypergraph")
:
returns the number of proteinssignature(r = "psimi25Hypergraph")
:
returns a data frame containing essential information of the interactorssignature(r = "psimi25Hypergraph")
:
returns the number of complexessignature(r = "matrix")
: returns the
hypergraph built from the incidence matrix
Tony Chiang <tchiang@ebi.ac.uk> , Jitao David Zhang <j.zhang@dkfz.de>
psimi25XML2Graph
,S4classpsimi25Graph-class
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]]