In ctlab/gatom: Finding an Active Metabolic Module in Atom Transition Network

gatom

An R-package for finding active metabolic modules in atom transition network.

Full vignette can be found here.

Installation

library(devtools)
install_github("ctlab/gatom")

Quick start

library(gatom)
library(data.table)
library(igraph)
library(mwcsr)

First let's load data with atom mappings (network object), enzyme annotations for mouse (org.Mm.eg.gatom) and metabolite annotations (met.kegg.db.rda):

data("networkEx")
data("org.Mm.eg.gatom.annoEx")
data("met.kegg.dbEx")

Loading input data:

data("met.de.rawEx")
data("gene.de.rawEx")

Getting atom graph:

g <- makeMetabolicGraph(network=networkEx,
                        topology = "atoms",
                        org.gatom.anno=org.Mm.eg.gatom.annoEx,
                        gene.de=gene.de.rawEx,
                        met.db=met.kegg.dbEx,
                        met.de=met.de.rawEx)
print(g)

Scoring graph, obtaining an instance of SGMWCS (Signal Generalized Maximum Weight Subgraph) problem instance:

gs <- scoreGraph(g, k.gene=25, k.met=25)

Initialize an SMGWCS solver (a heuristic relax-and-cut solver rnc_solver is used for simplicity, check out mwcsr package documentation for more options):

solver <- rnc_solver()

Finding a module:

res <- solve_mwcsp(solver, gs)
m <- res$graph

print(m)
head(E(m)$label)
head(V(m)$label)

We can save the module to different formats (dot, xgmml, svg, pdf):

saveModuleToPdf(m, file="M0.vs.M1.pdf", name="M0.vs.M1", n_iter=100, force=1e-5)

ctlab/gatom documentation built on May 3, 2024, 3:44 p.m.