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

Documentation for package ‘KEGGgraph’ version 1.69.0

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-- E --

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

-- G --

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

-- I --

isHomoList

Determines whether a list is homogenous

-- K --

KEGGEdge-class	Class 'KEGGEdge'
KEGGEdgeSubtype	KEGG edge subtypes
KEGGEdgeSubType-class	Class "KEGGEdgeSubType"
KEGGEdgeType	KEGG edge types
KEGGGraphics-class	class 'KEGGGraphics'
KEGGgraphLegend	Plot KEGG graph with Rgraphviz
KEGGGroup-class	Class "KEGGGroup"
KEGGNode-class	Class "KEGGNode"
KEGGNodeType	KEGG node types
KEGGPATHID2NAME	KEGG pathway identifier to name
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

-- M --

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

-- N --

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

-- P --

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

-- 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-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

-- 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