mchernigovskaya / gatom

Finding an Active Metabolic Module in Atom Transition Network

gatom

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

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Full vignette can be found here.

Installation

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

Quick start

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

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 <- makeAtomGraph(network=networkEx,
                   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:

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

Finding a module:

set.seed(42)
m <- solveSgmwcsRandHeur(gs, max.iterations = 2000)

print(m)
E(m)$label
V(m)$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, seed=1)