logical, should only the genes are maintained and
other types of nodes (compounds, etc) neglected? TRUE by default
expandGenes
logical, should homologue proteins expanded? TRUE
by default
Details
When 'expandGenes=TRUE', the nodes have unique names of KEGGID (in the form of 'org:xxxx', for example
'hsa:1432'), otherwise an auto-increment index given by KEGG is used
as node names. In the latter case, the node names are duplicated and
graphs cannot be simply merged before the nodes are unique.
KEGG node and edge data is stored in 'nodeData' and 'edgeData' slots
respectively, which can be extracted by getKEGGnodeData
and getKEGGedgeData.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(KEGGgraph)
Attaching package: 'KEGGgraph'
The following object is masked from 'package:graphics':
plot
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGGgraph/KEGGpathway2Graph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: KEGGpathway2Graph
> ### Title: Parses KEGGpathway to graph
> ### Aliases: KEGGpathway2Graph
>
> ### ** Examples
>
> sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
> kegg.pathway <- parseKGML(sfile)
> gR.compact<- KEGGpathway2Graph(kegg.pathway,expandGenes=FALSE)
>
>
>
>
>
> dev.off()
null device
1
>