# KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

## Documentation for package ‘KEGGgraph’ version 1.1.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

E G I K M N P Q R S T

## -- E --

edges,KEGGPathway,ANY-method | Class "KEGGPathway"
edges,KEGGPathway-method | Class "KEGGPathway"
edges<- | Class "KEGGPathway"
edges<-,KEGGPathway-method | Class "KEGGPathway"
entryID<- | Class "KEGGNode"
entryID<-,KEGGEdge-method | Class 'KEGGEdge'
entryID<-,KEGGNode-method | Class "KEGGNode"
expandKEGGNode | Expand KEGG node of paralogues
expandKEGGPathway | Expand KEGG Pathway

## -- G --

getComponent | Class "KEGGGroup"
getComponent,KEGGGroup-method | Class "KEGGGroup"
getComponent,KEGGNode-method | Class "KEGGNode"
getDisplayName | Get a character string as label for display
getDisplayName,graph-method | Get a character string as label for display
getDisplayName,KEGGNode-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,KEGGEdge-method | Get entry ID for single or list of KEGGNode or KEGGedge object(s)
getEntryID,KEGGNode-method | Get entry ID for single or list of KEGGNode or KEGGedge object(s)
getEntryID,list-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,character-method | Get KEGG gene link
getKEGGgeneLink-methods | Get KEGG gene link
getKEGGID | Get KEGG ID
getKEGGID,KEGGNode-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,KEGGEdge-method | Class 'KEGGEdge'
getName,KEGGEdgeSubType-method | Class "KEGGEdgeSubType"
getName,KEGGEdgeSubtype-method | Get 'name' attribute
getName,KEGGNode-method | Get 'name' attribute
getName,KEGGPathway-method | Class "KEGGPathway"
getName,KEGGPathwayInfo-method | Get 'name' attribute
getName,KEGGReaction-method | Class "KEGGReaction"
getName-methods | Get 'name' attribute
getNamedElement | Extract the value in a vector by name
getPathwayInfo | Get KEGG pathway info
getPathwayInfo,KEGGPathway-method | Get KEGG pathway info
getPathwayInfo-methods | Get KEGG pathway info
getProduct | Class "KEGGReaction"
getProduct,KEGGReaction-method | Class "KEGGReaction"
getReactions | Get KEGG reactions
getReactions,KEGGPathway-method | Get KEGG reactions
getReactions-methods | Get KEGG reactions
getRgraphvizEdgeNames | Get Rgraphviz compatitable edge names
getSubstrate | Class "KEGGReaction"
getSubstrate,KEGGReaction-method | Class "KEGGReaction"
getSubtype | Get subtype
getSubtype,graph-method | Get subtype
getSubtype,KEGGEdge-method | Get subtype
getSubtype-methods | Get subtype
getTitle | Get title for given element
getTitle,KEGGPathway-method | Class "KEGGPathway"
getTitle,KEGGPathway-method | Class "KEGGPathway"
getTitle,KEGGPathwayInfo-method | Class "KEGGPathwayInfo"
getTitle-methods | Get title for given element
getType | Get type attribute
getType,KEGGEdge-method | Get type attribute
getType,KEGGNode-method | Get type attribute
getType,KEGGReaction-method | Get type attribute
getType-methods | Get type attribute
getValue | Get 'value' attribute
getValue,KEGGEdgeSubType-method | Class "KEGGEdgeSubType"
getValue,KEGGEdgeSubtype-method | Get 'value' attribute
getValue-methods | Get 'value' attribute
graphDensity | Graph density

## -- I --

isHomoList | Determines whether a list is homogenous

## -- K --

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

## -- M --

mergeGraphs | A function to merge KEGG graphs
mergeKEGGgraphs | Merge KEGG graphs, also merging KEGGNode and KEGGEdge attributes

## -- N --

name<- | Class "KEGGNode"
name<-,KEGGNode-method | Class "KEGGNode"
neighborhood | Return the neighborhood set of given vertices
nodes,KEGGPathway-method | Class "KEGGPathway"
nodes<-,KEGGPathway,ANY-method | Class "KEGGPathway"

## -- P --

parseEntry | Parse ENTRY elements of KGML document
parseGraphics | Parse 'graphics' elements in KGML files
parseKGML | KGML file parser
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

## -- Q --

queryKEGGsubgraph | Query the subgraph of a given KEGG graph with Entrez GeneID (s)

## -- R --

randomSubGraph | Randomly subset the given graph
retrieveKGML | Get KGML file (url) with KEGG PATHWAY ID and (optional) organism

## -- S --

setKEGGedgeData | Get or set list of KEGG node or edge data
setKEGGnodeData | Get or set list of KEGG node or edge data
show,KEGGEdge-method | Class 'KEGGEdge'
show,KEGGEdgeSubType-method | Class "KEGGEdgeSubType"
show,KEGGNode-method | Class "KEGGNode"
show,KEGGPathway-method | Class "KEGGPathway"
show,KEGGPathwayInfo-method | Class "KEGGPathwayInfo"
show,KEGGReaction-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,graph-method | Get display information for relation subtypes
subtypeDisplay,KEGGEdge-method | Get display information for relation subtypes
subtypeDisplay,KEGGEdgeSubType-method | Get display information for relation subtypes
subtypeDisplay-methods | Get display information for relation subtypes

## -- T --

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