Annotation and identification of the KEGG pathways.


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Documentation for package ‘SubpathwayMiner’ version 1.1

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background The Background Genes.
cutoffAnn Get the statistically significantly enriched pathways
dGraph Directed graph list constructed from KEGG metabolic pathways
ec2gene A list that maps Enzyme Commission numbers to gene identifiers
gene2ec A list that maps gene identifiers to Enzyme Commission numbers
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
getDefaultBackground Get the default background genes
getDefaultGraph Get relationship between KEGG pathways and genes
getDefaultMetabolicPathway Get an identifier list of the default metabolic pathways
getDefaultUndirectedGraph Get the default undirected graph
getEnzymeFromGene Get a list of enzymes from a list of genes
getGeneFromEnzyme Get a list of genes from a list of enzymes
getGeneFromPathway Get genes from pathways
getKcsmpAnn Get the sub-pathways annotation and identification of metabolic network
getKcSubGraph Mine sub-pathways from the version of metabolic pathways
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
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
printAnn Print the results of pathway annotation and identification
saveKe2g ke2g environment function
uGraph The undirected graph list constructed from KEGG metabolic pathways
updateGraphs Update graphs constructed from KEGG metabolic pathways
updateOrgAndIdType Update the organism and the type of gene identifier