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

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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.

Author
Jitao David Zhang, with inputs from Paul Shannon
Date of publication
None
Maintainer
Jitao David Zhang <jitao_david.zhang@roche.com>
License
GPL (>= 2)
Version
1.32.0
URLs

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