Package 'KEGGgraph' - Bioconductor

More documents

Recommendations

Info

6 getKEGGID-methods getKEGGgeneLink-methods Get KEGG gene link Description Tranlsate a object into a link point to the gene on KEGG website. This method complies with the Gene link rule of the KEGG website. Methods object = "character" A KEGGID, for example ’hsa:1423’ Examples getKEGGgeneLink("hsa:1423") getKEGGID-methods Get KEGG ID Description Get KEGGID from a KEGGNode-class object. The KEGGNode-class can be either another pathway (KEGGID in the form like ’hsa\d*’), KEGG Gene (’hsa:\d*’) or compound (’cpd:C\d*’). In case of the KEGG Gene ID, the organism prefix is removed when the value is returned. Methods object = "KEGGNode" An object of KEGGNode-class Examples wntfile
getKEGGnodeData 7 getKEGGnodeData Get or set list of KEGG node or edge data Description The ’get’ methods extracts KEGG node (edge) attributes from a graph produced by calling parseKGML2Graph or KEGGpathway2Graph. The ’set’ methods writes a list into the edge or node data. Usage getKEGGnodeData(graph, n) getKEGGedgeData(graph, n) Arguments graph n a graph object by parsing KGML file, where KEGG node and edge attributes are maintained optional character string, name of the desired node or edge. If is missing all node Data is returned Details Node and edge data is stored as list within environments in graphs to save memory and speed up graph manipulations. When using getKEGGnodeData or getKEGGedgeData is called, the list is extracted out of the environment and returned. Value Either a list or single item of KEGGNode-class or KEGGEdge-class object(s). Note These functions will be unified into ’KEGGnodeData’ and ’KEGGnodeData
Page 1 and 2: Package ‘KEGGgraph’ May 22, 201
Page 3 and 4: expandKEGGNode 3 queryKEGGsubgraph
Page 5: getEntryID-methods 5 Examples sfile
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 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 (

Package 'KEGGgraph' - Bioconductor

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?