Entry: KEGGEdge-class
Aliases: KEGGEdge-class show,KEGGEdge-method entryID<-,KEGGEdge-method getName,KEGGEdge-method
Keywords: classes
Description: Class 'KEGGEdge'
URL: ../../../library/KEGGgraph/html/KEGGEdge-class.html

Entry: KEGGEdgeSubType-class
Aliases: KEGGEdgeSubType-class getName,KEGGEdgeSubType-method getValue,KEGGEdgeSubType-method show,KEGGEdgeSubType-method
Keywords: classes
Description: Class "KEGGEdgeSubType"
URL: ../../../library/KEGGgraph/html/KEGGEdgeSubType-class.html

Entry: KEGGEdgeSubtype
Aliases: KEGGEdgeType KEGGNodeType KEGGEdgeSubtype
Keywords: datasets
Description: Predefinitions of node or edge types
URL: ../../../library/KEGGgraph/html/KEGGEdgeSubtype.html

Entry: KEGGGraphics-class
Aliases: KEGGGraphics-class
Keywords: classes
Description: class 'KEGGGraphics'
URL: ../../../library/KEGGgraph/html/KEGGGraphics-class.html

Entry: KEGGGroup-class
Aliases: KEGGGroup-class getComponent getComponent,KEGGGroup-method
Keywords: classes
Description: Class "KEGGGroup"
URL: ../../../library/KEGGgraph/html/KEGGGroup-class.html

Entry: KEGGNode-class
Aliases: KEGGNode-class show,KEGGNode-method name<-,KEGGNode-method name<- entryID<- entryID<-,KEGGNode-method getComponent,KEGGNode-method
Keywords: classes
Description: Class "KEGGNode"
URL: ../../../library/KEGGgraph/html/KEGGNode-class.html

Entry: KEGGPathway-class
Aliases: KEGGPathway-class edges,KEGGPathway,ANY-method edges<- edges<-,KEGGPathway-method getName,KEGGPathway-method getTitle,KEGGPathway-method nodes<-,KEGGPathway,ANY-method nodes,KEGGPathway-method edges,KEGGPathway-method show,KEGGPathway-method getTitle,KEGGPathway-method
Keywords: classes
Description: Class "KEGGPathway"
URL: ../../../library/KEGGgraph/html/KEGGPathway-class.html

Entry: KEGGPathwayInfo-class
Aliases: KEGGPathwayInfo-class getTitle,KEGGPathwayInfo-method show,KEGGPathwayInfo-method
Keywords: classes
Description: Class "KEGGPathwayInfo"
URL: ../../../library/KEGGgraph/html/KEGGPathwayInfo-class.html

Entry: KEGGReaction-class
Aliases: KEGGReaction-class show,KEGGReaction-method getName,KEGGReaction-method getSubstrate getSubstrate,KEGGReaction-method getProduct getProduct,KEGGReaction-method
Keywords: classes
Description: Class "KEGGReaction"
URL: ../../../library/KEGGgraph/html/KEGGReaction-class.html

Entry: KEGGpathway2Graph
Aliases: KEGGpathway2Graph
Keywords: 
Description: Parses KEGGpathway to graph
URL: ../../../library/KEGGgraph/html/KEGGpathway2Graph.html

Entry: KEGGpathway2reactionGraph
Aliases: KEGGpathway2reactionGraph
Keywords: 
Description: Convert chemical reaction network of KEGG pathway into graph
URL: ../../../library/KEGGgraph/html/KEGGpathway2reactionGraph.html

Entry: expandKEGGNode
Aliases: expandKEGGNode
Keywords: 
Description: Expand KEGG node of paralogues
URL: ../../../library/KEGGgraph/html/expandKEGGNode.html

Entry: expandKEGGPathway
Aliases: expandKEGGPathway
Keywords: 
Description: Expand KEGG Pathway
URL: ../../../library/KEGGgraph/html/expandKEGGPathway.html

Entry: getDisplayName-methods
Aliases: getDisplayName getDisplayName-methods getDisplayName,KEGGNode-method getDisplayName,graph-method
Keywords: methods
Description: Get a character string as label for display
URL: ../../../library/KEGGgraph/html/getDisplayName-methods.html

Entry: getEntryID-methods
Aliases: getEntryID getEntryID-methods getEntryID,KEGGEdge-method getEntryID,KEGGNode-method getEntryID,list-method
Keywords: methods
Description: Get entry ID for single or list of KEGGNode or KEGGedge object(s)
URL: ../../../library/KEGGgraph/html/getEntryID-methods.html

Entry: getKEGGID-methods
Aliases: getKEGGID getKEGGID-methods getKEGGID,KEGGNode-method
Keywords: methods
Description: Get KEGG ID
URL: ../../../library/KEGGgraph/html/getKEGGID-methods.html

Entry: getKEGGgeneLink-methods
Aliases: getKEGGgeneLink getKEGGgeneLink-methods getKEGGgeneLink,character-method
Keywords: methods
Description: Get KEGG gene link
URL: ../../../library/KEGGgraph/html/getKEGGgeneLink-methods.html

Entry: getKEGGnodeData
Aliases: getKEGGnodeData setKEGGnodeData getKEGGedgeData setKEGGedgeData
Keywords: 
Description: Get or set list of KEGG node or edge data
URL: ../../../library/KEGGgraph/html/getKEGGnodeData.html

Entry: getKGMLurl
Aliases: getKGMLurl retrieveKGML
Keywords: IO
Description: Get KGML file (url) with KEGG PATHWAY ID and (optional) organism
URL: ../../../library/KEGGgraph/html/getKGMLurl.html

Entry: getName-methods
Aliases: getName getName-methods getName,KEGGEdgeSubtype-method getName,KEGGNode-method getName,KEGGPathwayInfo-method
Keywords: methods
Description: Get 'name' attribute
URL: ../../../library/KEGGgraph/html/getName-methods.html

Entry: getNamedElement
Aliases: getNamedElement
Keywords: 
Description: Extract the value in a vector by name
URL: ../../../library/KEGGgraph/html/getNamedElement.html

Entry: getPathwayInfo-methods
Aliases: getPathwayInfo getPathwayInfo-methods getPathwayInfo,KEGGPathway-method
Keywords: methods
Description: Get KEGG pathway info
URL: ../../../library/KEGGgraph/html/getPathwayInfo-methods.html

Entry: getReactions-methods
Aliases: getReactions getReactions-methods getReactions,KEGGPathway-method
Keywords: methods
Description: Get KEGG reactions
URL: ../../../library/KEGGgraph/html/getReactions-methods.html

Entry: getRgraphvizEdgeNames
Aliases: getRgraphvizEdgeNames
Keywords: 
Description: Get Rgraphviz compatitable edge names
URL: ../../../library/KEGGgraph/html/getRgraphvizEdgeNames.html

Entry: getSubtype-methods
Aliases: getSubtype getSubtype-methods getSubtype,graph-method getSubtype,KEGGEdge-method
Keywords: methods
Description: Get subtype
URL: ../../../library/KEGGgraph/html/getSubtype-methods.html

Entry: getTitle-methods
Aliases: getTitle getTitle-methods
Keywords: methods
Description: Get title for given element
URL: ../../../library/KEGGgraph/html/getTitle-methods.html

Entry: getType-methods
Aliases: getType getType-methods getType,KEGGEdge-method getType,KEGGNode-method getType,KEGGReaction-method
Keywords: methods
Description: Get type attribute
URL: ../../../library/KEGGgraph/html/getType-methods.html

Entry: getValue-methods
Aliases: getValue getValue-methods getValue,KEGGEdgeSubtype-method
Keywords: methods
Description: Get 'value' attribute
URL: ../../../library/KEGGgraph/html/getValue-methods.html

Entry: graphDensity
Aliases: graphDensity
Keywords: 
Description: Graph density
URL: ../../../library/KEGGgraph/html/graphDensity.html

Entry: isHomoList
Aliases: isHomoList
Keywords: 
Description: Determines whether a list is homogenous
URL: ../../../library/KEGGgraph/html/isHomoList.html

Entry: kgmlFileName2PathwayName
Aliases: kgmlFileName2PathwayName
Keywords: 
Description: Convert KGML file name to pathway name
URL: ../../../library/KEGGgraph/html/kgmlFileName2PathwayName.html

Entry: mergeGraphs
Aliases: mergeGraphs
Keywords: 
Description: A function to merge KEGG graphs
URL: ../../../library/KEGGgraph/html/mergeGraphs.html

Entry: mergeKEGGgraphs
Aliases: mergeKEGGgraphs
Keywords: 
Description: Merge KEGG graphs, also merging KEGGNode and KEGGEdge attributes
URL: ../../../library/KEGGgraph/html/mergeKEGGgraphs.html

Entry: neighborhood
Aliases: neighborhood
Keywords: 
Description: Return the neighborhood set of given vertices
URL: ../../../library/KEGGgraph/html/neighborhood.html

Entry: parseEntry
Aliases: parseEntry
Keywords: IO
Description: Parse ENTRY elements of KGML document
URL: ../../../library/KEGGgraph/html/parseEntry.html

Entry: parseGraphics
Aliases: parseGraphics
Keywords: 
Description: Parse 'graphics' elements in KGML files
URL: ../../../library/KEGGgraph/html/parseGraphics.html

Entry: parseKGML
Aliases: parseKGML
Keywords: 
Description: KGML file parser
URL: ../../../library/KEGGgraph/html/parseKGML.html

Entry: parseKGML2Graph
Aliases: parseKGML2Graph
Keywords: 
Description: Parse KGML files into KEGG graph
URL: ../../../library/KEGGgraph/html/parseKGML2Graph.html

Entry: parseKGMLexpandMaps
Aliases: parseKGMLexpandMaps
Keywords: 
Description: A convenient function to parse KGML and expand its containing maps into one graph object
URL: ../../../library/KEGGgraph/html/parseKGMLexpandMaps.html

Entry: parsePathwayInfo
Aliases: parsePathwayInfo
Keywords: IO
Description: Parse information of the pathway from KGML files
URL: ../../../library/KEGGgraph/html/parsePathwayInfo.html

Entry: parseReaction
Aliases: parseReaction
Keywords: IO
Description: Parse reaction from KGML files
URL: ../../../library/KEGGgraph/html/parseReaction.html

Entry: parseRelation
Aliases: parseRelation
Keywords: IO
Description: Parse RELATION elements from KGML files
URL: ../../../library/KEGGgraph/html/parseRelation.html

Entry: parseSubType
Aliases: parseSubType
Keywords: 
Description: Parse KGML relation subtype
URL: ../../../library/KEGGgraph/html/parseSubType.html

Entry: plotKEGGgraph
Aliases: plotKEGGgraph KEGGgraphLegend
Keywords: 
Description: Plot KEGG graph with Rgraphviz
URL: ../../../library/KEGGgraph/html/plotKEGGgraph.html

Entry: pvalue2asterisk
Aliases: pvalue2asterisk
Keywords: 
Description: Return common significance sign (asterisk) associated with given p value
URL: ../../../library/KEGGgraph/html/pvalue2asterisk.html

Entry: queryKEGGsubgraph
Aliases: queryKEGGsubgraph
Keywords: 
Description: Query the subgraph of a given KEGG graph with Entrez GeneID (s)
URL: ../../../library/KEGGgraph/html/queryKEGGsubgraph.html

Entry: randomSubGraph
Aliases: randomSubGraph
Keywords: 
Description: Randomly subset the given graph
URL: ../../../library/KEGGgraph/html/randomSubGraph.html

Entry: splitKEGGgroup
Aliases: splitKEGGgroup
Keywords: 
Description: Split KEGG group
URL: ../../../library/KEGGgraph/html/splitKEGGgroup.html

Entry: subGraphByNodeType
Aliases: subGraphByNodeType
Keywords: 
Description: Subset KEGG graph by node types
URL: ../../../library/KEGGgraph/html/subGraphByNodeType.html

Entry: subKEGGgraph
Aliases: subKEGGgraph
Keywords: 
Description: Subset KEGG graph, including subsetting node and edge attributes
URL: ../../../library/KEGGgraph/html/subKEGGgraph.html

Entry: subtypeDisplay-methods
Aliases: subtypeDisplay subtypeDisplay-methods subtypeDisplay,graph-method subtypeDisplay,KEGGEdge-method subtypeDisplay,KEGGEdgeSubType-method
Keywords: methods
Description: Get display information for relation subtypes
URL: ../../../library/KEGGgraph/html/subtypeDisplay-methods.html

Entry: top
Aliases: top
Keywords: datasets
Description: Colorectal cancer dataset
URL: ../../../library/KEGGgraph/html/top.html

Entry: translateKEGGID2GeneID
Aliases: translateKEGGID2GeneID translateKEGG2GeneID translateGeneID2KEGGID
Keywords: 
Description: Translate between KEGGID and Entrez Gene ID
URL: ../../../library/KEGGgraph/html/translateKEGGID2GeneID.html

Entry: translateKEGGgraph
Aliases: translateKEGGgraph
Keywords: 
Description: Tranlate the KEGG graph from being indexed by KEGGID to another identifer
URL: ../../../library/KEGGgraph/html/translateKEGGgraph.html
