- Page 1 and 2: Package ‘WGCNA’ March 6, 2009 V
- 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: lockwiseConsensusModules 13 Details
- Page 15 and 16: lockwiseConsensusModules 15 scaleQu
- Page 17 and 18: lockwiseConsensusModules 17 For eac
- Page 19 and 20: lockwiseModules 19 blockwiseModules
- Page 21 and 22: lockwiseModules 21 minCoreKMESize s
- Page 23 and 24: checkAdjMat 23 References Bin Zhang
- Page 25 and 26: clusterCoef 25 clusterCoef Clusteri
- Page 27 and 28: consensusOrderMEs 27 Arguments MEs
- Page 29 and 30: consensusProjectiveKMeans 29 Usage
- Page 31 and 32: cor1 31 Arguments x Value Note use
- Page 33 and 34: 0.2. WARNING 33 0.2 Warning .... Au
- Page 35 and 36: correlationPreservation 35 correlat
- Page 37 and 38: displayColors 37 Arguments dendro c
- Page 39 and 40: exportNetworkToCytoscape 39 exportN
- Page 41 and 42: fixDataStructure 41 fixDataStructur
- Page 43 and 44: goodGenes 43 Value A logical vector
- Page 45 and 46: goodSamplesGenes 45 Details Value T
- Page 47 and 48: goodSamples 47 Arguments multiExpr
- Page 49 and 50: greenBlackRed 49 greenBlackRed Gree
- Page 51 and 52: hubGeneSignificance 51 References Y
- Page 53 and 54: intramodularConnectivity 53 } print
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labeledBarplot 55 See Also checkSet
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labeledHeatmap 57 Details Value yCo
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labels2colors 59 main = "Mix-labele
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mergeCloseModules 61 mergeCloseModu
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moduleColor.getMEprefix 63 dendro o
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moduleEigengenes 65 Details Value s
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moduleNumber 67 moduleNumber Fixed-
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multiSetMEs 69 nPC align excludeGre
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nearestNeighborConnectivityMS 71 va
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nearestNeighborConnectivity 73 Argu
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networkScreeningGS 75 networkScreen
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networkScreening 77 } diag(datKMEBa
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0.4. WARNING 79 Examples ##---- Sho
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normalizeLabels 81 normalizeLabels
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orderMEs 83 See Also labels2colors
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pickHardThreshold 85 pickHardThresh
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plotClusterTreeSamples 87 verbose i
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plotColorUnderTree 89 cex.dendroLab
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plotDendroAndColors 91 Usage plotDe
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plotEigengeneNetworks 93 coloredBar
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plotMEpairs 95 See Also labeledHeat
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plotNetworkHeatmap 97 See Also barp
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preservationNetworkConnectivity 99
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projectiveKMeans 101 networkType ne
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andIndex 103 randIndex function to
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ecutBlockwiseTrees 105 Usage recutB
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ecutBlockwiseTrees 107 Details Valu
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ecutConsensusTrees 109 TOMFiles den
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edWhiteGreen 111 Note unmergedColor
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0.6. WARNING 113 Note further notes
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scaleFreePlot 115 scaleFreePlot Vis
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sigmoidAdjacencyFunction 117 See Al
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signumAdjacencyFunction 119 signumA
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simulateDatExpr 121 simulateDatExpr
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simulateEigengeneNetwork 123 and ef
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simulateModule 125 Arguments ME Det
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0.7. WARNING 127 Details If necessa
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simulateSmallLayer 129 Arguments or
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standardColors 131 Arguments Value
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TOMplot 133 TOMplot Graphical repre
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TOMsimilarity 135 References Bin Zh
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vectorTOM 137 References Bin Zhang
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0.8. WARNING 139 Details If necessa
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0.9. WARNING 141 Warning .... Note
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WGCNA-package 143 checkAdjMat Check
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WGCNA-package 145 simulateMultiExpr
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INDEX 147 multiSetMEs, 65 nearestNe
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INDEX 149 WGCNA (WGCNA-package), 13