KEGGPathway-class: Class "KEGGPathway"

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

Class "KEGGPathway"

Description

A class to represent KEGG pathway

Objects from the Class

Objects can be created by calls of the form new("KEGGPathway", ...) . Normally they are created by parseKGML.

Slots

pathwayInfo:

An object of KEGGPathwayInfo-class

nodes:

List of objects of KEGGNode-class

edges:

List of objects of KEGGEdge-class

reactions:

List of objects of KEGGReaction-class

Methods

edges

signature(object = "KEGGPathway", which = "ANY"): KEGGEdges of the pathway

edges<-

signature(object = "KEGGPathway"): setting edges

getName

signature(object = "KEGGPathway"): getting pathway name

getTitle

signature(object = "KEGGPathway"): getting pathway title

nodes<-

signature(object = "KEGGPathway", value = "ANY"): setting nodes

nodes

signature(object = "KEGGPathway"): KEGGNodes of the pathway

getPathwayInfo

signature(object = "KEGGPathway"): getting KEGGPathwayInfo

getTitle

signature(object = "KEGGPathway"): getting title of the pathway

show

signature(object = "KEGGPathway"): display method

Author(s)

Jitao David Zhang mailto:[e-mail]

References

KGML Document manual https://www.genome.jp/kegg/docs/xml/

See Also

parseKGML, KEGGEdge-class, KEGGNode-class, KEGGReaction-class

Examples

## We show how to extract information from KEGGPathway objects
## Parse KGML file into a 'KEGGPathway' object
mapfile <- system.file("extdata/map00260.xml", package="KEGGgraph")
maptest <- parseKGML(mapfile)

## short summary of the pathway
maptest

## get information of the pathway
getPathwayInfo(maptest)

## nodes of the pathway
nodes <- nodes(maptest)
node <- nodes[[3]]
getName(node)
getType(node)
getDisplayName(node)

## edges of the pathway
edges <- edges(maptest)
edge <- edges[[3]]
getEntryID(edge)
getSubtype(edge)

Accio/KEGGgraph documentation built on Jan. 13, 2023, 1:03 p.m.