Package 'KEGGgraph' - Bioconductor

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36 parseKGML References KGML Document manual http://www.genome.jp/kegg/docs/xml/ See Also KEGGGraphics-class parseKGML KGML file parser Description The function parses KGML files according to the KGML XML documentation. Usage parseKGML(file) Arguments file Name of KGML file Details Value The function parses KGML file (depending on XML package). An object of KEGGPathway-class. Author(s) Jitao David Zhang mailto:jitao_david.zhang@roche.com References See Also KGML Manual http://www.genome.jp/kegg/docs/xml/ parseEntry, parseRelation, parseReaction, KEGGPathway-class, Examples sfile
parseKGML2DataFrame 37 parseKGML2DataFrame Parse KGML file into a data frame Description This function extends the parseKGML2Graph function, by converting the resulting graph into a threecolumn data frame representing out-nodes (the from column in the data frame), in-nodes (to) and subtypes of edges that connect them (subtype). It can be used, for example, for exporting KEGG pathway networks in plain text files. Usage parseKGML2DataFrame(file, reactions=FALSE,...) Arguments file reactions A KGML file Logical, whether metabolic reactions should be parsed and returned as part of the data frame. Default:FALSE ... Other parameters passed to KEGGpathway2Graph Details The out- and in-nodes are represented in the form of KEGG identifiers. For human EntrezIDs the function translateKEGGID2GeneID can be used. Multile edges are supported: in case more than one subtypes of edges exist between two nodes, they are all listed in the resulting data frame. Value A three-column data frame, representing the graph structure: out-nodes (the from column), in-nodes (to) and edge subtype (subtype). Author(s) Jitao David Zhang See Also parseKGML2Graph, KEGGpathway2Graph and translateKEGGID2GeneID.
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: parseGraphics 35 Details See http:/
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 and 48: splitKEGGgroup 47 splitKEGGgroup Sp
Page 49 and 50: subtypeDisplay-methods 49 Arguments
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 (

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