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KEGGgraph (version 1.30.0)

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

Description

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.

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Version

Version

1.30.0

License

GPL (>= 2)

Maintainer

Jitao David Zhang

Last Published

February 15th, 2017

Functions in KEGGgraph (1.30.0)

parseRelation

Parse RELATION elements from KGML files
getTitle-methods

Get title for given element
parseKGML

KGML file parser
KEGGGroup-class

Class "KEGGGroup"
expandKEGGNode

Expand KEGG node of paralogues
graphDensity

Graph density
isHomoList

Determines whether a list is homogenous
translateKEGGID2GeneID

Translate between KEGGID and Entrez Gene ID
splitKEGGgroup

Split KEGG group
subGraphByNodeType

Subset KEGG graph by node types
translateKEGGgraph

Tranlate the KEGG graph from being indexed by KEGGID to another identifer
KEGGpathway2Graph

Parses KEGGpathway to graph
parseSubType

Parse KGML relation subtype
KEGGEdgeSubtype

Predefinitions of node or edge types
plotKEGGgraph

Plot KEGG graph with Rgraphviz
top

Colorectal cancer dataset
subtypeDisplay-methods

Get display information for relation subtypes
getDisplayName-methods

Get a character string as label for display
getKEGGnodeData

Get or set list of KEGG node or edge data
KEGGPathwayInfo-class

Class "KEGGPathwayInfo"
getRgraphvizEdgeNames

Get Rgraphviz compatitable edge names
parseReaction

Parse reaction from KGML files
getSubtype-methods

Get subtype
KEGGReaction-class

Class "KEGGReaction"
expandKEGGPathway

Expand KEGG Pathway
parseGraphics

Parse 'graphics' elements in KGML files
subKEGGgraph

Subset KEGG graph, including subsetting node and edge attributes
getValue-methods

Get 'value' attribute
getNamedElement

Extract the value in a vector by name
parseKGML2Graph

Parse KGML files into KEGG graph
parseKGMLexpandMaps

A convenient function to parse KGML and expand its containing maps into one graph object
queryKEGGsubgraph

Query the subgraph of a given KEGG graph with Entrez GeneID (s)
parseEntry

Parse ENTRY elements of KGML document
neighborhood

Return the neighborhood set of given vertices
randomSubGraph

Randomly subset the given graph
KEGGEdge-class

Class 'KEGGEdge'
KEGGEdgeSubType-class

Class "KEGGEdgeSubType"
KEGGpathway2reactionGraph

Convert chemical reaction network of KEGG pathway into graph
getKEGGgeneLink-methods

Get KEGG gene link
KEGGGraphics-class

class 'KEGGGraphics'
getName-methods

Get 'name' attribute
getKEGGID-methods

Get KEGG ID
getType-methods

Get type attribute
getEntryID-methods

Get entry ID for single or list of KEGGNode or KEGGedge object(s)
parseKGML2DataFrame

Parse KGML file into a data frame
mergeKEGGgraphs

Merge KEGG graphs, also merging KEGGNode and KEGGEdge attributes
KEGGNode-class

Class "KEGGNode"
KEGGPathway-class

Class "KEGGPathway"
parsePathwayInfo

Parse information of the pathway from KGML files
getPathwayInfo-methods

Get KEGG pathway info
getKGMLurl

Get KGML file (url) with KEGG PATHWAY ID and (optional) organism
getReactions-methods

Get KEGG reactions
mergeGraphs

A function to merge KEGG graphs
pvalue2asterisk

Return common significance sign (asterisk) associated with given p value
kgmlFileName2PathwayName

Convert KGML file name to pathway name