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 |