updateGraphs {SubpathwayMiner}R Documentation

Update graphs constructed from KEGG metabolic pathways

Description

Update graphs constructed from KEGG metabolic pathways.

Usage

   updateGraphs(pathwayList=getDefaultMetabolicPathway(),
               path="ftp://ftp.genome.jp/pub/kegg/xml/map/",verbose=TRUE)

Arguments

pathwayList A character vector of the KEGG metabolic pathway identifiers.
path A character string.
verbose A logical. If TRUE, the additional diagnostics are printed.

Details

The function is able to update the graph variable uGraph and dGraph in the environment variable of the system.

We construct and update the simplification version of metabolic pathways by extracting relations from the XML data of metabolic pathways. The XML data is available from the FTP site. ftp://ftp.genome.jp/pub/kegg/xml/map/

The argument pathwayList is a character vector of the KEGG metabolic pathway identifiers. The default value is provided by the return value of getDefaultMetabolicPathway. The user can change the value for constructing the subset of the graphs of the KEGG pathways.

Note that if one needs to use the updated graphs in the future, one should run the function saveKe2g to save the setting. Detailed information is provided in saveKe2g and loadKe2g.

Note that the programming is likely to be time consumming.

Author(s)

Chunquan Li <lcqbio@yahoo.com.cn>

See Also

uGraph, dGraph,getDefaultMetabolicPathway,updateOrgAndIdType

Examples

##construct the graphs list of Nucleotide Metabolism which include two pathways.
#It is considered as the subset of pathways of interest.
#updateGraphs(pathwayList=c("path:00230","path:00240"))

#get their sub-pathways
#subpathways<-getKcSubGraph(k=5,getDefaultUndirectedGraph())

#annotate genes to these sub-pathways to identify sub-pathway
##get a example of gene list
#data(gene2path)
#geneList<-names(gene2path)[1:1000]
#ann<-getAnn(geneList,graphList=subpathways)
#printAnn(ann)[2:5]

#visualize a sub-pathway of these sub-pathways
#plot(subpathways[[1]])


[Package SubpathwayMiner version 1.1 Index]