A software package for annotation and identification of the KEGG pathways.


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Documentation for package ‘SubpathwayMiner’ version 3.1

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cutoffAnn Get the statistically significantly enriched pathways
gene2ec The environment variable of the system
gene2ko The environment variable of the system
gene2path The environment variable of the system
generateNetwork Generate disease-metabolic subpathway networks
getAexample Get a set of genes
getAnn Annotate a set of genes to pathways or sub-pathways based on enzyme commission (EC)
getDefaultBackground Get the default background genes
getDefaultGraph Get relationship between KEGG pathways and genes
getDefaultKOPathway Get an identifier list of the default pathways based on KEGG Orthology (KO)
getDefaultKOUndirectedGraph Get the default undirected graph based on KEGG Orthology
getDefaultMetabolicPathway Get an identifier list of the default metabolic pathways
getDefaultUndirectedGraph Get the default undirected graph based onenzyme commission (EC) numbers
getEnzymeFromGene Map between two types of identifiers
getEnzymeFromKGene Map between two types of identifiers
getGeneFromEnzyme Map between two types of identifiers
getGeneFromKGene Map between two types of identifiers
getGeneFromKO Map between two types of identifiers
getGeneFromPathway Map between two types of identifiers
getKcsmpAnn Get the sub-pathways annotation and identification of metabolic network
getKcSubGraph Mine sub-pathways
getKGeneFromEnzyme Map between two types of identifiers
getKGeneFromGene Map between two types of identifiers
getKGeneFromKO Map between two types of identifiers
getKGeneFromPathway Map between two types of identifiers
getKOAnn Annotate a set of genes to sub-pathways by using KEGG Orthology (KO)
getKOFromGene Map between two types of identifiers
getKOFromKGene Map between two types of identifiers
getMpAnn get annotation informations of metabolic pathways
getOrgAndIdType Get the type of organism and identifier in the current environment variable
getPathwayFromGene Map between two types of identifiers
getPathwayFromKGene Map between two types of identifiers
getPIdFromPName Map between two types of identifiers
getPNameFromPId Map between two types of identifiers
gotoKEGG Visualize pathways or sub-pathways through linking to the KEGG web site
ke2g The environment variable of the system
keggpathid2name The environment variable of the system
KOuGraph The environment variable of the system
kpidList The environment variable of the system
loadKe2g ke2g environment function
map_title The environment variable of the system
mpidList The environment variable of the system
plotAnn Visualize pathways or sub-pathways based on enzyme commission (EC) numbers
plotKOAnn Visualize pathways or sub-pathways based on KEGG Orthology (KO)
printAnn Print the results of pathway annotation and identification
saveKe2g ke2g environment function
uGraph The environment variable of the system
updateGraphs Update graphs constructed from KEGG metabolic pathways
updateKOGraphs Update graphs based on based on KEGG Orthology (KO) constructed from KEGG pathways
updateOrgAndIdType Update the organism and the type of gene identifier