buildPCHypergraph {RpsiXML} | R Documentation

## Build protein complex hypergraph from PSI-MI 2.5 files

### Description

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.

### Usage

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

### Arguments

`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`

### Details

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

### Value

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.

### Author(s)

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

### See Also

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

### Examples

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

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

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

[Package RpsiXML version 2.34.0 Index]