getEntryID-methods: Get entry ID for single or list of KEGGNode or KEGGedge...

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

Description

The method extracts EntryIDs from KEGGNode-class or KEGGEdge-class object(s).

In case of KEGGEdge-class objects, the entryID of the nodes involved in the binary are returned as a vector in the order specified by the direction of the relation, that is, if the edge is defined as A->B, then the entryID returned from the edge equals to c(getEntryID(A), getEntryID(B)).

Methods

obj = "KEGGEdge"

Object of KEGGEdge-class

obj = "list"

A wrapper for list of KEGGNode-class or KEGGEdge-class objects

Author(s)

Jitao David Zhang mailto:[e-mail]

References

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

Examples

sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
pathway <- parseKGML(sfile)

nodes <- nodes(pathway)
node <- nodes[[7]]
getEntryID(node)

edges <- edges(pathway)
edge <- edges[[7]]
getEntryID(edge)

getEntryID(nodes[1:4])
getEntryID(edges[1:4])

Example output

Attaching package: 'KEGGgraph'

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

    plot

[1] "7"
Entry1ID Entry2ID 
    "35"     "31" 
[1] "1" "2" "3" "4"
     Entry1ID Entry2ID
[1,] "47"     "40"    
[2,] "46"     "40"    
[3,] "45"     "40"    
[4,] "44"     "39"    

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