Man pages for Bioconductor-mirror/KEGGgraph
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

expandKEGGNodeExpand KEGG node of paralogues
expandKEGGPathwayExpand KEGG Pathway
getDisplayName-methodsGet a character string as label for display
getEntryID-methodsGet entry ID for single or list of KEGGNode or KEGGedge...
getKEGGgeneLink-methodsGet KEGG gene link
getKEGGID-methodsGet KEGG ID
getKEGGnodeDataGet or set list of KEGG node or edge data
getKGMLurlGet KGML file (url) with KEGG PATHWAY ID and (optional)...
getNamedElementExtract the value in a vector by name
getName-methodsGet 'name' attribute
getPathwayInfo-methodsGet KEGG pathway info
getReactions-methodsGet KEGG reactions
getRgraphvizEdgeNamesGet Rgraphviz compatitable edge names
getSubtype-methodsGet subtype
getTitle-methodsGet title for given element
getType-methodsGet type attribute
getValue-methodsGet 'value' attribute
graphDensityGraph density
isHomoListDetermines whether a list is homogenous
KEGGEdge-classClass 'KEGGEdge'
KEGGEdgeSubtypePredefinitions of node or edge types
KEGGEdgeSubType-classClass "KEGGEdgeSubType"
KEGGGraphics-classclass 'KEGGGraphics'
KEGGGroup-classClass "KEGGGroup"
KEGGNode-classClass "KEGGNode"
KEGGpathway2GraphParses KEGGpathway to graph
KEGGpathway2reactionGraphConvert chemical reaction network of KEGG pathway into graph
KEGGPathway-classClass "KEGGPathway"
KEGGPathwayInfo-classClass "KEGGPathwayInfo"
KEGGReaction-classClass "KEGGReaction"
kgmlFileName2PathwayNameConvert KGML file name to pathway name
mergeGraphsA function to merge KEGG graphs
mergeKEGGgraphsMerge KEGG graphs, also merging KEGGNode and KEGGEdge...
neighborhoodReturn the neighborhood set of given vertices
parseEntryParse ENTRY elements of KGML document
parseGraphicsParse 'graphics' elements in KGML files
parseKGMLKGML file parser
parseKGML2DataFrameParse KGML file into a data frame
parseKGML2GraphParse KGML files into KEGG graph
parseKGMLexpandMapsA convenient function to parse KGML and expand its containing...
parsePathwayInfoParse information of the pathway from KGML files
parseReactionParse reaction from KGML files
parseRelationParse RELATION elements from KGML files
parseSubTypeParse KGML relation subtype
plotKEGGgraphPlot KEGG graph with Rgraphviz
pvalue2asteriskReturn common significance sign (asterisk) associated with...
queryKEGGsubgraphQuery the subgraph of a given KEGG graph with Entrez GeneID...
randomSubGraphRandomly subset the given graph
splitKEGGgroupSplit KEGG group
subGraphByNodeTypeSubset KEGG graph by node types
subKEGGgraphSubset KEGG graph, including subsetting node and edge...
subtypeDisplay-methodsGet display information for relation subtypes
topColorectal cancer dataset
translateKEGGgraphTranlate the KEGG graph from being indexed by KEGGID to...
translateKEGGID2GeneIDTranslate between KEGGID and Entrez Gene ID
Bioconductor-mirror/KEGGgraph documentation built on July 28, 2017, 4:22 a.m.