buildPCHypergraph: Build protein complex hypergraph from PSI-MI 2.5 files
In alyst/RpsiXML: R interface to PSI-MI 2.5 files

Description Usage Arguments Details Value Author(s) See Also Examples

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.

1	buildPCHypergraph(xmlFiles, psimi25source, split.by = c("none", "organismName", "taxId"), ...)

`xmlFiles`	PSI-MI 2.5 files, must be of complex mode.
`psimi25source`	PSI-MI 2.5 source indicator, for example INTACT.PSIMI25 for files from IntAct database
`split.by`	The qualifier to split the dataset, `none` specifies not to split the dataset, `organismName` and `taxId` splits the dataset according to organism name or taxonomy ID respectively. In the case of splitting, the results are a list of hypergraphs indexed by respective split qualifier
`...`	other parameters passed to `parsePsimi25Complex`

See psimi25Hypergraph-class for the use of resulting hypergraphs and examples.

In case the dataset is not split (by setting the option split.by as none, the result is a psimi25Hypergraph-class object. If the dataset was split, a list of psimi25Hypergraph-class is returned, which is indexed by either the organism name or the taxonomy ID.

Jitao David Zhang <jitao_david.zhang@roche.com>

psimi25Hypergraph-class for the use of hypergraph objects, separateXMLDataByExpt for similar functionality but for interaction mode files

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

pc2 <- buildPCHypergraph(intactComplexxml, INTACT.PSIMI25,split.by="organismName")

pc2[2]
complexes(pc2[[2]])[1:3]