buildPCHypergraph: 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

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.

Details

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

Examples

Run this code

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]