Finding an Active Metabolic Module in Atom Transition Network

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Documentation for package ‘gatom’ version 1.5.0

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