Finding an Active Metabolic Module in Atom Transition Network


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Documentation for package ‘gatom’ version 1.5.0

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