Annotation and identification of the KEGG pathways.


[Package List] [Top]

Documentation for package ‘SubpathwayMiner’ version 2.0

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

background The Background Genes.
cutoffAnn Get the statistically significantly enriched pathways
dGraph Directed graph list based on enzyme commission (EC) numbers constructed from KEGG metabolic pathways
ec2gene A list that maps Enzyme Commission (EC) numbers to gene identifiers
gene2ec A list that maps gene identifiers to Enzyme Commission (EC) numbers
gene2KO A list that maps gene identifiers to KEGG Orthology (KO)
gene2path A list that maps gene identifiers to KEGG pathway identifiers
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 Get a list of enzymes from a list of genes
getGeneFromEnzyme Get a list of genes from a list of enzymes
getGeneFromKO Get a list of genes from a list of KOs
getGeneFromPathway Get genes from pathways
getKcsmpAnn Get the sub-pathways annotation and identification of metabolic network
getKcSubGraph Mine sub-pathways
getKOAnn Annotate a set of genes to sub-pathways by using KEGG Orthology (KO)
getKOFromGene Get a list of KOs from a list of genes
getMpAnn get annotation informations of metabolic pathways
getOrgAndIdType Get the type of organism and identifier in the current environment variable
getPathwayFromGene Get pathwaysfrom genes
getPathwayNameFromId Get pathway name from identifier
gotoKEGG Visualize pathways or sub-pathways through linking to the KEGG web site
ke2g The environment variable of the system
keggpathid2name The data that maps KEGG pathway identifiers to names
KO2gene A list that maps KEGG Orthology (KO) to gene identifiers
KOuGraph The undirected graph list based on KEGG Orthology (KO) identifiers constructed from KEGG pathways
kpidList pathway identifier list based on KEGG Orthology (KO)
loadKe2g ke2g environment function
mpidList metabolic pathway identifier list
path2gene A list that maps KEGG pathway identifiers to gene identifiers
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 undirected graph list based on enzyme commission (EC) numbers constructed from KEGG metabolic pathways
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