KEGGEdge-class: Class 'KEGGEdge'

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

Description

A class to represent 'relation' elements in KGML files and edge objects in a KEGG graph

Objects from the Class

Objects are normally created by parseRelation function, which is not intended to be called by user directly

Slots

entry1ID:

The entryID of the first KEGGNode

entry2ID:

The entryID of the second KEGGNode

type:

The type of the relation, see getType-methods

subtype:

The subtype(s) of the edge, a list of KEGGEdgeSubType

Methods

getEntryID

signature(obj = "KEGGEdge"): Get entryIDs of the edge in the order specified by the direction of the edge

getType

signature(object = "KEGGEdge"): Get the relation type

getName

signature(object = "KEGGEdge"): Get the names of edges in the convention of Rgraphviz, 'node1~node2'

show

signature(object = "KEGGEdge"): Show method

Author(s)

Jitao David Zhang mailto:[e-mail]

References

KGML Manual http://www.genome.jp/kegg/docs/xml/

See Also

KEGGNode-class

Examples

mapfile<- system.file("extdata/map00260.xml", package="KEGGgraph")
maptest <- parseKGML(mapfile)

x <- edges(maptest)[[1]]
class(x)

## examples to extract information from KEGGEdge
getName(x)
getEntryID(x)

getType(x)
getSubtype(x)

subtype <- getSubtype(x)[[1]]
getName(subtype)

Example output

Attaching package: 'KEGGgraph'

The following object is masked from 'package:graphics':

    plot

[1] "KEGGEdge"
attr(,"package")
[1] "KEGGgraph"
[1] "17~34"
Entry1ID Entry2ID 
    "17"     "34" 
[1] "ECrel"
$subtype
  [ Subtype name ]: compound
  [ Subtype value ]: 96

[1] "compound"

KEGGgraph documentation built on Nov. 8, 2020, 5:42 p.m.