The class to present 'entry' element in KGML files and
nodes in KEGG graphs
Objects from the Class
Objects can be created by calls of the function parseEntry
and is not intended to be directly created by users.
Slots
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
Methods
getDisplayName
signature(object = "KEGGNode"): get
display name
getEntryID
signature(obj = "KEGGNode"): get entryID,
in case of gene-expanded graphs this is the same as getKEGGID
getKEGGID
signature(object = "KEGGNode"): get KEGGID
getType
signature(object = "KEGGNode"): get the type of
the node
<-name
signature(object = "KEGGNode"): replace name
getComponent
signature(obj = "KEGGNode"): returns
entryID (the same as getEntryID), for compatibility with KEGGGroup-class
## 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)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(KEGGgraph)
Attaching package: 'KEGGgraph'
The following object is masked from 'package:graphics':
plot
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGGgraph/KEGGNode-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: KEGGNode-class
> ### Title: Class "KEGGNode"
> ### Aliases: KEGGNode-class show,KEGGNode-method name<-,KEGGNode-method
> ### name<- entryID<- entryID<-,KEGGNode-method
> ### getComponent,KEGGNode-method
> ### Keywords: classes
>
> ### ** Examples
>
> ## 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)
KEGG Node (Entry '1'):
------------------------------------------------------------
[ displayName ]: C00338
[ Name ]: cpd:C00338
[ Type ]: compound
[ Link ]: http://www.genome.jp/dbget-bin/www_bget?compound+C00338
------------------------------------------------------------
> getName(node)
[1] "cpd:C00338"
> getDisplayName(node)
[1] "C00338"
> getEntryID(node)
[1] "1"
> getKEGGID(node)
[1] "C00338"
>
>
>
>
>
> dev.off()
null device
1
>