Package 'KEGGgraph' - Bioconductor

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48 subKEGGgraph subGraphByNodeType Subset KEGG graph by node types Description The function subsets KEGG graph by node types, mostly used in extracting gene networks. Usage subGraphByNodeType(graph, type = "gene", kegg=TRUE) Arguments graph type kegg A KEGG graph object produced by calling parseKGML2Graph node type, see KEGGNodeType for details logical, should the KEGG Node and Edge attributes be maintained during the subsetting By default set to ’TRUE’ Value A subgraph of the original graph Author(s) Jitao David Zhang mailto:jitao_david.zhang@roche.com Examples sfile
subtypeDisplay-methods 49 Arguments nodes graph Node names to subset A graph parsed from KGML files, produced by parseKGML2Graph, KEGGpathway2Graph or parseKGMLexpandMaps Details Value subGraph does not subset the node or edge attributes, hence the results of getKEGGnodeData and getKEGGedgeData does not map to the nodes and edges in the subgraph in a one-to-one manner, with attributes of removed nodes and edges still remaining in the subGraph. subKEGGgraph calls subGraph first to subset the graph, and then it also subsets the KEGGnodeData and KEGGedgeData so that they are one-to-one mapped to the nodes and edges in the subgraph. A graph with nodeData and edgeData. Author(s) Jitao David Zhang mailto:jitao_david.zhang@roche.com Examples sfile
Page 1 and 2: Package ‘KEGGgraph’ May 22, 201
Page 3 and 4: expandKEGGNode 3 queryKEGGsubgraph
Page 5 and 6: getEntryID-methods 5 Examples sfile
Page 7 and 8: getKEGGnodeData 7 getKEGGnodeData G
Page 9 and 10: getName-methods 9 Note So far the f
Page 11 and 12: getPathwayInfo-methods 11 Arguments
Page 13 and 14: getRgraphvizEdgeNames 13 getRgraphv
Page 15 and 16: getType-methods 15 Examples sfile
Page 17 and 18: isHomoList 17 Examples tnodes
Page 19 and 20: KEGGEdgeSubtype 19 Examples mapfile
Page 21 and 22: KEGGGraphics-class 21 KEGGGraphics-
Page 23 and 24: KEGGNode-class 23 KEGGNode-class Cl
Page 25 and 26: KEGGpathway2Graph 25 getPathwayInfo
Page 27 and 28: KEGGpathway2reactionGraph 27 Descri
Page 29 and 30: KEGGReaction-class 29 Examples sfil
Page 31 and 32: mergeGraphs 31 mergeGraphs A functi
Page 33 and 34: neighborhood 33 Examples sfile
Page 35 and 36: parseGraphics 35 Details See http:/
Page 37 and 38: parseKGML2DataFrame 37 parseKGML2Da
Page 39 and 40: parseKGMLexpandMaps 39 Examples sfi
Page 41 and 42: parseReaction 41 parseReaction Pars
Page 43 and 44: plotKEGGgraph 43 plotKEGGgraph Plot
Page 45 and 46: queryKEGGsubgraph 45 queryKEGGsubgr
Page 47: splitKEGGgroup 47 splitKEGGgroup Sp
Page 51 and 52: translateKEGGID2GeneID 51 Details T
Page 53 and 54: Index ∗Topic IO getKGMLurl, 8 par
Page 55: INDEX 55 nodes,KEGGPathway-method (

Package 'KEGGgraph' - Bioconductor

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