Package 'KEGGgraph' - Bioconductor

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44 pvalue2asterisk KEGGgraphLegend() par(opar) pvalue2asterisk Return common significance sign (asterisk) associated with given p value Description A p-value of 0.05, 0.01, 0.001 correspond to one, two or three asterisks. If ’sig.1’ is set to TRUE, then the p-value of 0.1 returns ’.’. Usage pvalue2asterisk(pvalues, sig.1 = FALSE) Arguments pvalues sig.1 A numeric value logical, whether the significance sign of 0.1 should be returned Value A character string containing the signs Author(s) Jitao David Zhang mailto:jitao_david.zhang@roche.com Examples pvalue2asterisk(0.03) pvalue2asterisk(0.007) pvalue2asterisk(3e-5) pvalue2asterisk(0.55)
queryKEGGsubgraph 45 queryKEGGsubgraph Query the subgraph of a given KEGG graph with Entrez GeneID (s) Description Given a list of genes (identified by Entrez GeneID), the function subsets the given KEGG gragh of the genes as nodes (and maintaining all the edges between). Usage queryKEGGsubgraph(geneids, graph, organism = "hsa", addmissing = FALSE) Arguments geneids graph organism addmissing A vector of Entrez GeneIDs A KEGG graph a three-alphabet code of organism logical, in case the given gene is not found in the graph, should it be added as single node to the subgraph Details This function solves the questions like ’How is the list of gene interact with each other in the context of pathways’ Limited by the translateKEGGID2GeneID, this function supports only human for now. We are working to include other organisms. If ’addmissing’ is set to TRUE, the missing gene in the given list will be added to the returned subgraph as single nodes. Value A subgraph with nodes representing genes and edges representing interactions. Author(s) Jitao David Zhang See Also translateGeneID2KEGGID
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: plotKEGGgraph 43 plotKEGGgraph Plot
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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