KEGGNode-class | R Documentation |
The class to present 'entry' element in KGML files and nodes in KEGG graphs
Objects can be created by calls of the function parseEntry
and is not intended to be directly created by users.
entryID
: entryID, the 'id' attribute of 'entry'
elements in KGML files. In each KGML file the entryID is specified
by auto-increment integers, therefore entryIDs from two individual
KGML files are not unique. However, if 'expandGenes' option is
specified in KEGGpathway2Graph
function, the unique
KEGGID will replace the default integer as the new entryID, which is
unique in biological context
name
:Name of the node
type
:Type of the node, use data(KEGGNodeType)
to see available values
link
:URL link of the node
reaction
:Reaction of the node
map
:Map of the node
graphics
:Graphic details (including display name) of
the node, an object of KEGGGraphics
signature(object = "KEGGNode")
: get
display name
signature(obj = "KEGGNode")
: get entryID,
in case of gene-expanded graphs this is the same as getKEGGID
signature(object = "KEGGNode")
: get KEGGID
signature(object = "KEGGNode")
: get the type of
the node
signature(object = "KEGGNode")
: replace name
signature(obj = "KEGGNode")
: returns
entryID (the same as getEntryID
), for compatibility with KEGGGroup-class
signature(object = "KEGGNode")
: show method
Jitao David Zhang mailto:jitao_david.zhang@roche.com
KGML Document manual https://www.genome.jp/kegg/docs/xml/
KEGGEdge-class
, parseEntry
## We show how to extract information from KEGGNode object sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph") pathway <- parseKGML(sfile) ns <- nodes(pathway) node <- ns[[1]] show(node) getName(node) getDisplayName(node) getEntryID(node) getKEGGID(node)
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