# Finding an Active Metabolic Module in Atom Transition Network

## Documentation for package ‘gatom’ version 1.9.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

abbreviateLabels | Abbreviate lipid labels for lipid module
addHighlyExpressedEdges | Add reactions without highly changing genes but with high average expression
collapseAtomsIntoMetabolites | Collapse atoms belonging to the same metabolite into one vertex
connectAtomsInsideMetabolite | Connect atoms belonging to the same metabolite with edges
createShinyCyJSWidget | Creates shinyCyJS widget from module
gene.de.rawEx | Example gene differential expression data.
getGeneDEMeta | Finds columns in gene differential expression table required for gatom analysis
getMetabolicPathways | Generate list of metabolic pathways from Reactome and KEGG databases
getMetDEMeta | Finds columns in differential expression table for metabolites required for gatom analysis
gEx | Example metabolic graph with atom topology.
gsEx | Example scored metabolic graph with atom topology.
makeMetabolicGraph | Creates metabolic graph based on specified data
makeOrgGatomAnnotation | Create an organism annotation object for network analysis
met.de.rawEx | Example metabolite differential abundance data.
met.kegg.dbEx | Example KEGG-based metabolite database object
mEx | Example metabolic module.
networkEx | Example KEGG-based network object
org.Mm.eg.gatom.annoEx | Example organism annotation object
prepareDE | Makes data.table with differential expression results containing all columns required for gatom and in the expected format based on metadata object
saveModuleToDot | Save module to a graphviz dot file
saveModuleToHtml | Save module to a html widget
saveModuleToPdf | Save module to a nice pdf file
saveModuleToXgmml | Save module to an XGMML file
scoreGraph | Score metabolic graph