The package can implement the graph-based reconstruction, analyses, and visualization of the KEGG pathways.


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Documentation for package ‘iSubpathwayMiner’ version 2.0

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iSubpathwayMiner-package The iSubpathwayMiner package
expandNode Expand nodes according to the type of nodes
filterNode filter node according to node type
gene2ec The variables in the environment variable k2ri of the system
gene2ko The variables in the environment variable k2ri of the system
getBackground Get the background
getEnzymeFromGene Map between identifiers
getEnzymeFromKGene Map between identifiers
getEnzymeFromSymbol Map between identifiers
getExample Get a set of components
getGeneFromEnzyme Map between identifiers
getGeneFromKGene Map between identifiers
getGeneFromKO Map between identifiers
getGeneFromPathway Map between identifiers
getGeneFromSymbol Map between identifiers
getKcSubiGraph Mine subpathways
getKGeneFromEnzyme Map between identifiers
getKGeneFromGene Map between identifiers
getKGeneFromKO Map between identifiers
getKGeneFromPathway Map between identifiers
getKGeneFromSymbol Map between identifiers
getKOFromGene Map between identifiers
getKOFromKGene Map between identifiers
getKOFromSymbol Map between identifiers
getMetabolicCOCOEMGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicCOCOGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicCOCOUEMGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicCOCOUGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicECCOEMGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicECCOGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicECCOUEMGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicECCOUGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicECECEMGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicECECGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicECECUEMGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicECECUGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicGEGEEMGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicGEGEUEMGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicGraph Convert metabolic pathways to graphs
getMetabolicKOCOEMGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicKOCOGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicKOCOUEMGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicKOCOUGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicKOKOEMGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicKOKOGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicKOKOUEMGraph Get pathway graphs using the combination of graph conversion functions
getMetabolicKOKOUGraph Get pathway graphs using the combination of graph conversion functions
getNodeLabel Get new node labels according to names attributes of graph
getNonMetabolicGEGEEMGraph Get pathway graphs using the combination of graph conversion functions
getNonMetabolicGEGEUEMGraph Get pathway graphs using the combination of graph conversion functions
getNonMetabolicGraph Convert non-metabolic pathways to directed graphs
getNonMetabolicKOCOEMGraph Get pathway graphs using the combination of graph conversion functions
getNonMetabolicKOCOGraph Get pathway graphs using the combination of graph conversion functions
getNonMetabolicKOCOUEMGraph Get pathway graphs using the combination of graph conversion functions
getNonMetabolicKOCOUGraph Get pathway graphs using the combination of graph conversion functions
getNonMetabolicKOKOEMGraph Get pathway graphs using the combination of graph conversion functions
getNonMetabolicKOKOGraph Get pathway graphs using the combination of graph conversion functions
getNonMetabolicKOKOUEMGraph Get pathway graphs using the combination of graph conversion functions
getNonMetabolicKOKOUGraph Get pathway graphs using the combination of graph conversion functions
getOrgAndIdType Get the type of organism and identifier in the current environment variable
getOrgIdFromOrgName Map between identifiers
getOrgNameFromOrgId Map between identifiers
getPathway Convert KGML files to a list variable in R
getPathwayFromGene Map between identifiers
getPathwayFromKGene Map between identifiers
getPrioBackground Get the conservative background
getSimpleGraph Convert multiple graphs to simple graphs
getSymbolFromEnzyme Map between identifiers
getSymbolFromGene Map between identifiers
getSymbolFromKGene Map between identifiers
getSymbolFromKO Map between identifiers
getUGraph Convert pathways to undirected graphs
identifyGraph Annotate a set of components to pathway graphs and identify statistically significantly enriched pathway graphs
identifyTopo Topology-based pathway analysis of gene sets
importPathway Update or import pathway files
initializeK2ri initialize environment k2ri
iSubpathwayMiner The iSubpathwayMiner package
k2ri The variables in the environment variable k2ri of the system
keggGene2gene The variables in the environment variable k2ri of the system
loadK2ri Load and save the environment variable k2ri of the system
mapNode Map current organism-specific gene identifiers to nodes in pathway graphs
mergeNode Merge nodes with the same names
metabolicEC The variables in the environment variable k2ri of the system
metabolicKO The variables in the environment variable k2ri of the system
nonMetabolicKO The variables in the environment variable k2ri of the system
plotAnnGraph Visualize annotated pathway graphs
plotGraph visualize a pathway graph
printGraph Print the results of graph annotation and identification
printTopo Print the results of topology-based pathway analysis of gene sets
sampleComponent Generate a random component set
saveK2ri Load and save the environment variable k2ri of the system
simplifyGraph Simplify pathways to gene product graphs or compound graphs
updateCompound Update compound identifiers
updateOrgAndIdType Update the organism and the type of gene identifier
updatePathway Update or import pathway files
updateTaxonomy Update taxonomy