aafPathwayItem-class {annaffy}R Documentation

Class aafPathwayItem, a class for KEGG pathway id elements

Description

An abstraction for KEGG pathway id elements from Bioconductor data packages. Multiple instances of this class are held by the wrapper class aafPathway.

Objects from the Class

Objects are generally created by the aafPathway constructor. Objects can also be created manually by calls of the form new("aafPathwayItem", id, name, enzyme).

Slots

id:
Object of class character containing KEGG pathway id
name:
Object of class character containing textual name
enzyme:
Object of class character containing the Enzyme Commision number if applicable

Methods

getText
(aafPathwayItem): Returns textual representation formatted "id: name".
getURL
(aafPathwayItem): Returns a URL to the corresponding entry in the Kyoto Encyclopedia of Genes and Genomes database. If there is a corresponding EC number, it will be highlighted in red.
getHTML
(aafPathwayItem): Returns an HTML representation including the URL link and pathway name.

Author(s)

Colin A. Smith, annaffy@colinsmith.org

See Also

aafPathway-class, aafPathway


[Package annaffy version 1.2.0 Index]