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| edges-method | Class "KEGGPathway" |
| edges<- | Class "KEGGPathway" |
| edges<--method | Class "KEGGPathway" |
| entryID<- | Class "KEGGNode" |
| entryID<--method | Class 'KEGGEdge' |
| entryID<--method | Class "KEGGNode" |
| expandKEGGNode | Expand KEGG node of paralogues |
| expandKEGGPathway | Expand KEGG Pathway |
| getCategoryIndepKGMLurl | Get KGML file (url) with KEGG PATHWAY ID and (optional) organism |
| getComponent | Class "KEGGGroup" |
| getComponent-method | Class "KEGGGroup" |
| getComponent-method | Class "KEGGNode" |
| getDisplayName | Get a character string as label for display |
| getDisplayName-method | Get a character string as label for display |
| getDisplayName-methods | Get a character string as label for display |
| getEntryID | Get entry ID for single or list of KEGGNode or KEGGedge object(s) |
| getEntryID-method | Get entry ID for single or list of KEGGNode or KEGGedge object(s) |
| getEntryID-methods | Get entry ID for single or list of KEGGNode or KEGGedge object(s) |
| getKEGGedgeData | Get or set list of KEGG node or edge data |
| getKEGGgeneLink | Get KEGG gene link |
| getKEGGgeneLink-method | Get KEGG gene link |
| getKEGGgeneLink-methods | Get KEGG gene link |
| getKEGGID | Get KEGG ID |
| getKEGGID-method | Get KEGG ID |
| getKEGGID-methods | Get KEGG ID |
| getKEGGnodeData | Get or set list of KEGG node or edge data |
| getKGMLurl | Get KGML file (url) with KEGG PATHWAY ID and (optional) organism |
| getName | Get 'name' attribute |
| getName-method | Class 'KEGGEdge' |
| getName-method | Class "KEGGEdgeSubType" |
| getName-method | Class "KEGGPathway" |
| getName-method | Class "KEGGReaction" |
| getName-method | Get 'name' attribute |
| getName-methods | Get 'name' attribute |
| getNamedElement | Extract the value in a vector by name |
| getPathwayInfo | Get KEGG pathway info |
| getPathwayInfo-method | Get KEGG pathway info |
| getPathwayInfo-methods | Get KEGG pathway info |
| getProduct | Class "KEGGReaction" |
| getProduct-method | Class "KEGGReaction" |
| getReactions | Get KEGG reactions |
| getReactions-method | Get KEGG reactions |
| getReactions-methods | Get KEGG reactions |
| getRgraphvizEdgeNames | Get Rgraphviz compatitable edge names |
| getSubstrate | Class "KEGGReaction" |
| getSubstrate-method | Class "KEGGReaction" |
| getSubtype | Get subtype |
| getSubtype-method | Get subtype |
| getSubtype-methods | Get subtype |
| getTitle | Get title for given element |
| getTitle-method | Class "KEGGPathway" |
| getTitle-method | Class "KEGGPathwayInfo" |
| getTitle-methods | Get title for given element |
| getType | Get type attribute |
| getType-method | Get type attribute |
| getType-methods | Get type attribute |
| getValue | Get 'value' attribute |
| getValue-method | Class "KEGGEdgeSubType" |
| getValue-method | Get 'value' attribute |
| getValue-methods | Get 'value' attribute |
| graphDensity | Graph density |
| isHomoList | Determines whether a list is homogenous |
| KEGGEdge-class | Class 'KEGGEdge' |
| KEGGEdgeSubtype | Predefinitions of node or edge types |
| KEGGEdgeSubType-class | Class "KEGGEdgeSubType" |
| KEGGEdgeType | Predefinitions of node or edge types |
| KEGGGraphics-class | class 'KEGGGraphics' |
| KEGGgraphLegend | Plot KEGG graph with Rgraphviz |
| KEGGGroup-class | Class "KEGGGroup" |
| KEGGNode-class | Class "KEGGNode" |
| KEGGNodeType | Predefinitions of node or edge types |
| KEGGPathway-class | Class "KEGGPathway" |
| KEGGpathway2Graph | Parses KEGGpathway to graph |
| KEGGpathway2reactionGraph | Convert chemical reaction network of KEGG pathway into graph |
| KEGGPathwayInfo-class | Class "KEGGPathwayInfo" |
| KEGGReaction-class | Class "KEGGReaction" |
| kgmlFileName2PathwayName | Convert KGML file name to pathway name |
| kgmlNonmetabolicName2MetabolicName | Get KGML file (url) with KEGG PATHWAY ID and (optional) organism |
| mergeGraphs | A function to merge KEGG graphs |
| mergeKEGGgraphs | Merge KEGG graphs, also merging KEGGNode and KEGGEdge attributes |
| name<- | Class "KEGGNode" |
| name<--method | Class "KEGGNode" |
| neighborhood | Return the neighborhood set of given vertices |
| nodes-method | Class "KEGGPathway" |
| nodes<--method | Class "KEGGPathway" |
| 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 |
| retrieveKGML | Get KGML file (url) with KEGG PATHWAY ID and (optional) organism |
| setKEGGedgeData | Get or set list of KEGG node or edge data |
| setKEGGnodeData | Get or set list of KEGG node or edge data |
| show-method | Class 'KEGGEdge' |
| show-method | Class "KEGGEdgeSubType" |
| show-method | Class "KEGGNode" |
| show-method | Class "KEGGPathway" |
| show-method | Class "KEGGPathwayInfo" |
| show-method | Class "KEGGReaction" |
| splitKEGGgroup | Split KEGG group |
| subGraphByNodeType | Subset KEGG graph by node types |
| subKEGGgraph | Subset KEGG graph, including subsetting node and edge attributes |
| subtypeDisplay | Get display information for relation subtypes |
| subtypeDisplay-method | Get display information for relation subtypes |
| subtypeDisplay-methods | Get display information for relation subtypes |
| top | Colorectal cancer dataset |
| translateGeneID2KEGGID | Translate between KEGGID and Entrez Gene ID |
| translateKEGG2GeneID | Translate between KEGGID and Entrez Gene ID |
| translateKEGGgraph | Tranlate the KEGG graph from being indexed by KEGGID to another identifer |
| translateKEGGID2GeneID | Translate between KEGGID and Entrez Gene ID |