- Page 1 and 2: Package ‘WGCNA’ March 17, 2009
- Page 3: R topics documented: 3 plotClusterT
- Page 7 and 8: adjacency 7 Arguments datExpr selec
- Page 9 and 10: automaticNetworkScreeningGS 9 Argum
- Page 11 and 12: 0.1. WARNING 11 0.1 Warning .... Au
- Page 13 and 14: icor 13 nThreads verbose indent non
- Page 15 and 16: lockwiseConsensusModules 15 blocks
- Page 17 and 18: lockwiseConsensusModules 17 getTOMS
- Page 19 and 20: lockwiseConsensusModules 19 blockOr
- Page 21 and 22: lockwiseModules 21 randomSeed corTy
- Page 23 and 24: lockwiseModules 23 are then cluster
- Page 25 and 26: checkSets 25 Arguments adjMat min m
- Page 27 and 28: collectGarbage 27 collectGarbage It
- Page 29 and 30: consensusOrderMEs 29 consensusOrder
- Page 31 and 32: consensusProjectiveKMeans 31 useMea
- Page 33 and 34: 0.2. WARNING 33 Author(s) who you a
- Page 35 and 36: cor 35 cor Fast calculations of Pea
- Page 37 and 38: correlationPreservation 37 data = m
- Page 39 and 40: cutreeStatic 39 See Also hclust for
- Page 41 and 42: exportNetworkToCytoscape 41 Argumen
- Page 43 and 44: fixDataStructure 43 Arguments adjMa
- Page 45 and 46: goodGenesMS 45 Arguments multiExpr
- Page 47 and 48: goodSamplesGenesMS 47 Author(s) Pet
- Page 49 and 50: goodSamplesMS 49 Details This funct
- Page 51 and 52: greenBlackRed 51 Arguments datExpr
- Page 53 and 54: GTOMdist 53 Author(s) Peter Langfel
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Inline display of progress 55 Argum
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keepCommonProbes 57 Author(s) Steve
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labeledHeatmap 59 Value None. Autho
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labeledHeatmap 61 Examples # This e
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matchLabels 63 Examples labels = c(
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mergeCloseModules 65 Details Value
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moduleEigengenes 67 See Also module
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moduleEigengenes 69 averageExpr pre
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multiSetMEs 71 multiSetMEs Calculat
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multiSetMEs 73 Value From the user
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nearestNeighborConnectivity 75 samp
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networkConcepts 77 networkConcepts
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0.3. WARNING 79 Author(s) who you a
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0.4. WARNING 81 Arguments y Details
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0.4. WARNING 83 datMEBatch, use = "
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numbers2colors 85 numbers2colors Co
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overlapTable 87 Value A vector of l
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pickSoftThreshold 89 Author(s) Stev
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plotClusterTreeSamples 91 Usage plo
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plotDendroAndColors 93 Arguments De
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plotEigengeneNetworks 95 Details Va
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plotEigengeneNetworks 97 Details Va
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plotModuleSignificance 99 plotModul
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preservationNetworkConnectivity 101
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projectiveKMeans 103 pairwiseWeight
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propVarExplained 105 propVarExplain
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ecutBlockwiseTrees 107 See Also obj
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ecutBlockwiseTrees 109 minModuleSiz
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ecutConsensusTrees 111 recutConsens
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ecutConsensusTrees 113 Details Valu
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elativeCorPredictionSuccess 115 Val
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emoveGreyME 117 } if (sign1 == 0) s
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setCorrelationPreservation 119 setC
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signedKME 121 signedKME Signed eige
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simulateDatExpr5Modules 123 Usage s
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simulateDatExpr 125 backgroundNoise
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simulateModule 127 Arguments Detail
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simulateMultiExpr 129 See Also simu
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simulateSmallLayer 131 } nSamples =
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sizeGrWindow 133 sizeGrWindow Opens
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standardColors 135 standardColors C
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TOMsimilarityFromExpr 137 See Also
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unsignedAdjacency 139 Value A matri
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verboseBoxplot 141 corOptions type
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verboseScatterplot 143 Examples ##-
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WGCNA-package 145 } y = as.numeric(
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WGCNA-package 147 hubGeneSignifican
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Index ∗Topic kwd1 automaticNetwor
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INDEX 151 greenBlackRed, 48 greenWh