getSubtype-methods: Get subtype

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

Get subtype

Description

KEGG stores sub-type of interactions between entities in the KGML files, which can be extracted with this method. The descriptions for the subtypes can be explored at the KGML document manual in the references.

See KEGGEdge-class for examples. The method for graphs is a wrapper to extract all subtype information from one graph.

Methods

object = "graph"

A graph object of KEGGgraph. The method returns a list of subtypes in the same order of edges

object = "KEGGEdge"

An object of KEGGEdge, which stores the subtype information

Author(s)

Jitao David Zhang mailto:[e-mail]

References

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

Examples

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

edges <- edges(pathway)
subtype <- getSubtype(edges[[1]])
subtype

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