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

KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.

AuthorJitao David Zhang, with inputs from Paul Shannon
Date of publicationNone
MaintainerJitao David Zhang <jitao_david.zhang@roche.com>
LicenseGPL (>= 2)
Version1.32.0
http://www.nextbiomotif.com

View on Bioconductor

Man pages

expandKEGGNode: Expand KEGG node of paralogues

expandKEGGPathway: Expand KEGG Pathway

getDisplayName-methods: Get a character string as label for display

getEntryID-methods: Get entry ID for single or list of KEGGNode or KEGGedge...

getKEGGgeneLink-methods: Get KEGG gene link

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)...

getNamedElement: Extract the value in a vector by name

getName-methods: Get 'name' attribute

getPathwayInfo-methods: Get KEGG pathway info

getReactions-methods: Get KEGG reactions

getRgraphvizEdgeNames: Get Rgraphviz compatitable edge names

getSubtype-methods: Get subtype

getTitle-methods: Get title for given element

getType-methods: Get type 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"

KEGGGraphics-class: class 'KEGGGraphics'

KEGGGroup-class: Class "KEGGGroup"

KEGGNode-class: Class "KEGGNode"

KEGGpathway2Graph: Parses KEGGpathway to graph

KEGGpathway2reactionGraph: Convert chemical reaction network of KEGG pathway into graph

KEGGPathway-class: Class "KEGGPathway"

KEGGPathwayInfo-class: Class "KEGGPathwayInfo"

KEGGReaction-class: Class "KEGGReaction"

kgmlFileName2PathwayName: Convert KGML file name to pathway name

mergeGraphs: A function to merge KEGG graphs

mergeKEGGgraphs: Merge KEGG graphs, also merging KEGGNode and KEGGEdge...

neighborhood: Return the neighborhood set of given vertices

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...

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...

queryKEGGsubgraph: Query the subgraph of a given KEGG graph with Entrez GeneID...

randomSubGraph: Randomly subset the given graph

splitKEGGgroup: Split KEGG group

subGraphByNodeType: Subset KEGG graph by node types

subKEGGgraph: Subset KEGG graph, including subsetting node and edge...

subtypeDisplay-methods: Get display information for relation subtypes

top: Colorectal cancer dataset

translateKEGGgraph: Tranlate the KEGG graph from being indexed by KEGGID to...

translateKEGGID2GeneID: Translate between KEGGID and Entrez Gene ID

Functions

edges<- Man page
edges,KEGGPathway,ANY-method Man page
edges<-,KEGGPathway-method Man page
edges,KEGGPathway-method Man page
entryID<- Man page
entryID<-,KEGGEdge-method Man page
entryID<-,KEGGNode-method Man page
expandKEGGNode Man page
expandKEGGPathway Man page
getCategoryIndepKGMLurl Man page
getComponent Man page
getComponent,KEGGGroup-method Man page
getComponent,KEGGNode-method Man page
getDisplayName Man page
getDisplayName,graph-method Man page
getDisplayName,KEGGNode-method Man page
getDisplayName-methods Man page
getEntryID Man page
getEntryID,KEGGEdge-method Man page
getEntryID,KEGGNode-method Man page
getEntryID,list-method Man page
getEntryID-methods Man page
getKEGGedgeData Man page
getKEGGgeneLink Man page
getKEGGgeneLink,character-method Man page
getKEGGgeneLink-methods Man page
getKEGGID Man page
getKEGGID,KEGGNode-method Man page
getKEGGID-methods Man page
getKEGGnodeData Man page
getKGMLurl Man page
getName Man page
getNamedElement Man page
getName,KEGGEdge-method Man page
getName,KEGGEdgeSubtype-method Man page
getName,KEGGEdgeSubType-method Man page
getName,KEGGNode-method Man page
getName,KEGGPathwayInfo-method Man page
getName,KEGGPathway-method Man page
getName,KEGGReaction-method Man page
getName-methods Man page
getPathwayInfo Man page
getPathwayInfo,KEGGPathway-method Man page
getPathwayInfo-methods Man page
getProduct Man page
getProduct,KEGGReaction-method Man page
getReactions Man page
getReactions,KEGGPathway-method Man page
getReactions-methods Man page
getRgraphvizEdgeNames Man page
getSubstrate Man page
getSubstrate,KEGGReaction-method Man page
getSubtype Man page
getSubtype,graph-method Man page
getSubtype,KEGGEdge-method Man page
getSubtype-methods Man page
getTitle Man page
getTitle,KEGGPathwayInfo-method Man page
getTitle,KEGGPathway-method Man page
getTitle,KEGGPathway-method Man page
getTitle-methods Man page
getType Man page
getType,KEGGEdge-method Man page
getType,KEGGNode-method Man page
getType,KEGGReaction-method Man page
getType-methods Man page
getValue Man page
getValue,KEGGEdgeSubtype-method Man page
getValue,KEGGEdgeSubType-method Man page
getValue-methods Man page
graphDensity Man page
isHomoList Man page
KEGGEdge-class Man page
KEGGEdgeSubtype Man page
KEGGEdgeSubType-class Man page
KEGGEdgeType Man page
KEGGGraphics-class Man page
KEGGgraphLegend Man page
KEGGGroup-class Man page
KEGGNode-class Man page
KEGGNodeType Man page
KEGGpathway2Graph Man page
KEGGpathway2reactionGraph Man page
KEGGPathway-class Man page
KEGGPathwayInfo-class Man page
KEGGReaction-class Man page
kgmlFileName2PathwayName Man page
kgmlNonmetabolicName2MetabolicName Man page
mergeGraphs Man page
mergeKEGGgraphs Man page
name<- Man page
name<-,KEGGNode-method Man page
neighborhood Man page
nodes<-,KEGGPathway,ANY-method Man page
nodes,KEGGPathway-method Man page
parseEntry Man page
parseGraphics Man page
parseKGML Man page
parseKGML2DataFrame Man page
parseKGML2Graph Man page
parseKGMLexpandMaps Man page
parsePathwayInfo Man page
parseReaction Man page
parseRelation Man page
parseSubType Man page
plotKEGGgraph Man page
pvalue2asterisk Man page
queryKEGGsubgraph Man page
randomSubGraph Man page
retrieveKGML Man page
setKEGGedgeData Man page
setKEGGnodeData Man page
show,KEGGEdge-method Man page
show,KEGGEdgeSubType-method Man page
show,KEGGNode-method Man page
show,KEGGPathwayInfo-method Man page
show,KEGGPathway-method Man page
show,KEGGReaction-method Man page
splitKEGGgroup Man page
subGraphByNodeType Man page
subKEGGgraph Man page
subtypeDisplay Man page
subtypeDisplay,graph-method Man page
subtypeDisplay,KEGGEdge-method Man page
subtypeDisplay,KEGGEdgeSubType-method Man page
subtypeDisplay-methods Man page
top Man page
translateGeneID2KEGGID Man page
translateKEGG2GeneID Man page
translateKEGGgraph Man page
translateKEGGID2GeneID Man page

Files

KEGGgraph/ChangeLog
KEGGgraph/DESCRIPTION
KEGGgraph/Makefile
KEGGgraph/NAMESPACE
KEGGgraph/NEWS
KEGGgraph/R
KEGGgraph/R/annotation.R KEGGgraph/R/graph.R KEGGgraph/R/kegg2graph-functions.R KEGGgraph/R/kgmlfile.R KEGGgraph/R/misc.R KEGGgraph/R/parse.R KEGGgraph/R/vis.R
KEGGgraph/build
KEGGgraph/build/vignette.rds
KEGGgraph/data
KEGGgraph/data/KEGGEdgeSubtype.csv
KEGGgraph/data/KEGGEdgeType.csv
KEGGgraph/data/KEGGNodeType.csv
KEGGgraph/data/colorectalcancerSPIA.RData
KEGGgraph/inst
KEGGgraph/inst/CITATION
KEGGgraph/inst/doc
KEGGgraph/inst/doc/KEGGgraph.R
KEGGgraph/inst/doc/KEGGgraph.Rnw
KEGGgraph/inst/doc/KEGGgraph.pdf
KEGGgraph/inst/doc/KEGGgraphApp.R
KEGGgraph/inst/doc/KEGGgraphApp.Rnw
KEGGgraph/inst/doc/KEGGgraphApp.pdf
KEGGgraph/inst/extdata
KEGGgraph/inst/extdata/hsa00020.xml
KEGGgraph/inst/extdata/hsa04010.xml
KEGGgraph/inst/extdata/hsa04012.xml
KEGGgraph/inst/extdata/hsa04110.xml
KEGGgraph/inst/extdata/hsa04115.xml
KEGGgraph/inst/extdata/hsa04210.xml
KEGGgraph/inst/extdata/hsa04310.xml
KEGGgraph/inst/extdata/hsa04350.xml
KEGGgraph/inst/extdata/hsa04370.xml
KEGGgraph/inst/extdata/hsa04630.xml
KEGGgraph/inst/extdata/hsa05210.xml
KEGGgraph/inst/extdata/hsa05212.xml
KEGGgraph/inst/extdata/kgml-ed-toy.xml
KEGGgraph/inst/extdata/ko00051.xml
KEGGgraph/inst/extdata/map00260.xml
KEGGgraph/inst/unitTests
KEGGgraph/inst/unitTests/test_KEGGgraph.R
KEGGgraph/man
KEGGgraph/man/KEGGEdge-class.Rd KEGGgraph/man/KEGGEdgeSubType-class.Rd KEGGgraph/man/KEGGEdgeSubtype.Rd KEGGgraph/man/KEGGGraphics-class.Rd KEGGgraph/man/KEGGGroup-class.Rd KEGGgraph/man/KEGGNode-class.Rd KEGGgraph/man/KEGGPathway-class.Rd KEGGgraph/man/KEGGPathwayInfo-class.Rd KEGGgraph/man/KEGGReaction-class.Rd KEGGgraph/man/KEGGpathway2Graph.Rd KEGGgraph/man/KEGGpathway2reactionGraph.Rd KEGGgraph/man/expandKEGGNode.Rd KEGGgraph/man/expandKEGGPathway.Rd KEGGgraph/man/getDisplayName-methods.Rd KEGGgraph/man/getEntryID-methods.Rd KEGGgraph/man/getKEGGID-methods.Rd KEGGgraph/man/getKEGGgeneLink-methods.Rd KEGGgraph/man/getKEGGnodeData.Rd KEGGgraph/man/getKGMLurl.Rd KEGGgraph/man/getName-methods.Rd KEGGgraph/man/getNamedElement.Rd KEGGgraph/man/getPathwayInfo-methods.Rd KEGGgraph/man/getReactions-methods.Rd KEGGgraph/man/getRgraphvizEdgeNames.Rd KEGGgraph/man/getSubtype-methods.Rd KEGGgraph/man/getTitle-methods.Rd KEGGgraph/man/getType-methods.Rd KEGGgraph/man/getValue-methods.Rd KEGGgraph/man/graphDensity.Rd KEGGgraph/man/isHomoList.Rd KEGGgraph/man/kgmlFileName2PathwayName.Rd KEGGgraph/man/mergeGraphs.Rd KEGGgraph/man/mergeKEGGgraphs.Rd KEGGgraph/man/neighborhood.Rd KEGGgraph/man/parseEntry.Rd KEGGgraph/man/parseGraphics.Rd KEGGgraph/man/parseKGML.Rd KEGGgraph/man/parseKGML2DataFrame.Rd KEGGgraph/man/parseKGML2Graph.Rd KEGGgraph/man/parseKGMLexpandMaps.Rd KEGGgraph/man/parsePathwayInfo.Rd KEGGgraph/man/parseReaction.Rd KEGGgraph/man/parseRelation.Rd KEGGgraph/man/parseSubType.Rd KEGGgraph/man/plotKEGGgraph.Rd KEGGgraph/man/pvalue2asterisk.Rd KEGGgraph/man/queryKEGGsubgraph.Rd KEGGgraph/man/randomSubGraph.Rd KEGGgraph/man/splitKEGGgroup.Rd KEGGgraph/man/subGraphByNodeType.Rd KEGGgraph/man/subKEGGgraph.Rd KEGGgraph/man/subtypeDisplay-methods.Rd KEGGgraph/man/top.Rd KEGGgraph/man/translateKEGGID2GeneID.Rd KEGGgraph/man/translateKEGGgraph.Rd
KEGGgraph/tests
KEGGgraph/tests/kegg2graph.R
KEGGgraph/tests/testGraph.R
KEGGgraph/vignettes
KEGGgraph/vignettes/KEGGgraph.Rnw
KEGGgraph/vignettes/KEGGgraphApp.Rnw

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