KEGGEdge-class          Class 'KEGGEdge'
KEGGEdgeSubType-class   Class "KEGGEdgeSubType"
KEGGEdgeSubtype         KEGG edge subtypes
KEGGEdgeType            KEGG edge types
KEGGGraphics-class      class 'KEGGGraphics'
KEGGGroup-class         Class "KEGGGroup"
KEGGNode-class          Class "KEGGNode"
KEGGNodeType            KEGG node types
KEGGPATHID2NAME         KEGG pathway identifier to name
KEGGPathway-class       Class "KEGGPathway"
KEGGPathwayInfo-class   Class "KEGGPathwayInfo"
KEGGReaction-class      Class "KEGGReaction"
KEGGpathway2Graph       Parses KEGGpathway to graph
KEGGpathway2reactionGraph
                        Convert chemical reaction network of KEGG
                        pathway into graph
expandKEGGNode          Expand KEGG node of paralogues
expandKEGGPathway       Expand KEGG Pathway
getDisplayName-methods
                        Get a character string as label for display
getEntryID-methods      Get entry ID for single or list of KEGGNode or
                        KEGGedge object(s)
getKEGGID-methods       Get KEGG ID
getKEGGgeneLink-methods
                        Get KEGG gene link
getKEGGnodeData         Get or set list of KEGG node or edge data
getKGMLurl              Get KGML file (url) with KEGG PATHWAY ID and
                        (optional) organism
getName-methods         Get 'name' attribute
getNamedElement         Extract the value in a vector by name
getPathwayInfo-methods
                        Get KEGG pathway info
getReactions-methods    Get KEGG reactions
getRgraphvizEdgeNames   Get Rgraphviz compatitable edge names
getSubtype-methods      Get subtype
getTitle-methods        Get title for given element
getType-methods         Get type attribute
getValue-methods        Get 'value' attribute
graphDensity            Graph density
isHomoList              Determines whether a list is homogenous
kgmlFileName2PathwayName
                        Convert KGML file name to pathway name
mergeGraphs             A function to merge KEGG graphs
mergeKEGGgraphs         Merge KEGG graphs, also merging KEGGNode and
                        KEGGEdge attributes
neighborhood            Return the neighborhood set of given vertices
parseEntry              Parse ENTRY elements of KGML document
parseGraphics           Parse 'graphics' elements in KGML files
parseKGML               KGML file parser
parseKGML2DataFrame     Parse KGML file into a data frame
parseKGML2Graph         Parse KGML files into KEGG graph
parseKGMLexpandMaps     A convenient function to parse KGML and expand
                        its containing maps into one graph object
parsePathwayInfo        Parse information of the pathway from KGML
                        files
parseReaction           Parse reaction from KGML files
parseRelation           Parse RELATION elements from KGML files
parseSubType            Parse KGML relation subtype
plotKEGGgraph           Plot KEGG graph with Rgraphviz
pvalue2asterisk         Return common significance sign (asterisk)
                        associated with given p value
queryKEGGsubgraph       Query the subgraph of a given KEGG graph with
                        Entrez GeneID (s)
randomSubGraph          Randomly subset the given graph
splitKEGGgroup          Split KEGG group
subGraphByNodeType      Subset KEGG graph by node types
subKEGGgraph            Subset KEGG graph, including subsetting node
                        and edge attributes
subtypeDisplay-methods
                        Get display information for relation subtypes
top                     Colorectal cancer dataset
translateKEGGID2GeneID
                        Translate between KEGGID and Entrez Gene ID
translateKEGGgraph      Tranlate the KEGG graph from being indexed by
                        KEGGID to another identifer
