gatom: gatom: a package for finding an active metabolic module in...

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

gatom: a package for finding an active metabolic module in atom transition network

Description

This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.

Functions

Data preprocessing: prepareDE, getMetDEMeta, getGeneDEMeta

Graph creation: makeMetabolicGraph

Graph scoring: scoreGraph

Module postprocessing: collapseAtomsIntoMetabolites, connectAtomsInsideMetabolite, addHighlyExpressedEdges, abbreviateLabels

Plotting module: createShinyCyJSWidget

Exporting module: saveModuleToHtml, saveModuleToDot, saveModuleToPdf, saveModuleToXgmml

For detailed pipeline analysis, see gatom vignette: vignette("gatom-tutorial", package = "gatom")

Example Data

Example data provided by gatom consists of: metabolite differential abundance data (met.de.rawEx), gene differential expression data (gene.de.rawEx), KEGG-based network object (networkEx), KEGG-based metabolite database object (met.kegg.dbEx), Example organism annotation object (org.Mm.eg.gatom.annoEx), metabolic graph with atom topology (gEx), scored metabolic graph with atom topology (gsEx), and metabolic module (mEx).

ctlab/gatom documentation built on Oct. 22, 2023, 4:30 p.m.