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

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 Lefts and Rights. 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)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(NetPathMiner)
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/NetPathMiner/biopax2igraph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: biopax2igraph
> ### Title: Processes BioPAX objects into igraph objects
> ### Aliases: biopax2igraph
> 
> ### ** 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)
+ }
Loading required package: rBiopaxParser
Loading required package: data.table
Processing BioPAX (level 3) object as a metabolic network: 20 reactions found.
Processing BioPAX (level 3) object as a signaling network: 13 interaction found.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>