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

Files in this package

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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