biopax2igraph {NetPathMiner} | R Documentation

## Processes BioPAX objects into igraph objects

### Description

This function takes BioPAX objects (level 2 or 3) as input, and returns either a metabolic or a signaling network as output.

### Usage

    biopax2igraph(biopax, parse.as = c("metabolic", "signaling"),
      expand.complexes = FALSE, inc.sm.molecules = FALSE, verbose = TRUE)

### Arguments

`biopax` | BioPAX object generated by `readBiopax`.
`parse.as` | Whether to process file into a metabolic or a signaling network.
`expand.complexes` | Split protein complexes into individual gene nodes. Ignored if `parse.as="metabolic"`.
`inc.sm.molecules` | Include small molecules that are participating in signaling events. Ignored if `parse.as="metabolic"`.
`verbose` | Whether to display the progress of the function.

### Details

This function requires `rBiopaxParser` installed.

Users can specify whether files are processes as metabolic or signaling networks.

Metabolic networks are given as bipartite graphs, where metabolites and reactions represent vertex types. Reactions are constructed from `Conversion` classes, connecting them to their corresponding `Left`s and `Right`s. Each reaction vertex has `genes` attribute, listing all `Catalysis` relationships of this reaction. As a general rule, reactions inherit all annotation attributes of its catalyzig genes.

Signaling network have genes as vertices and edges represent interactions, such as activiation / inhibition. Genes participating in successive reactions are also connected. Signaling interactions are constructed from `Control` classes, where edges are drawn from `controller` to `controlled`.

All annotation attributes are exracted from `XRefs` associated with the vertices, and are stored according to MIRIAM guidelines (`miraim.db`, where db is the database name).

### Value

An igraph object, representing a metbolic or a signaling network.

### Author(s)

Ahmed Mohamed

### See Also

Other Database extraction methods: `KGML2igraph`, `SBML2igraph`

### Examples

    if(require(rBiopaxParser)){
        data(ex_biopax)
        # Process biopax as a metabolic network
        g <- biopax2igraph(ex_biopax)
        plotNetwork(g)

        # Process SBML file as a signaling network
        g <- biopax2igraph(ex_biopax, parse.as="signaling", expand.complexes=TRUE)
    }

[Package NetPathMiner version 1.16.0 Index]