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- Page 6 and 7: 6 WGCNA-packageblockwiseConsensusMo
- Page 8 and 9: 8 WGCNA-packageneighbors across mul
- Page 10 and 11: 10 accuracyMeasuresReferencesPeter
- Page 12 and 13: 12 addGridValueNone.Author(s)Steve
- Page 14 and 15: 14 adjacencyArgumentsmultiMEmultiTr
- Page 16 and 17: 16 adjacency.polyRegAuthor(s)Peter
- Page 18 and 19: 18 adjacency.splineRegUsageadjacenc
- Page 20 and 21: 20 alignExprSee AlsomutualInfoAdjac
- Page 22 and 23: 22 automaticNetworkScreeningArgumen
- Page 24 and 25: 24 bicorAuthor(s)Steve HorvathSee A
- Page 26 and 27: 26 bicorAndPvalueValueThe choice "a
- Page 28 and 29: 28 blockwiseConsensusModulesblockwi
- Page 30 and 31: 30 blockwiseConsensusModules# Gener
- Page 32 and 33: 32 blockwiseConsensusModulesgetTOMS
- Page 34 and 35: 34 blockwiseConsensusModules(in all
- Page 36 and 37: 36 blockwiseIndividualTOMsblockwise
- Page 38 and 39: 38 blockwiseIndividualTOMsDetailsne
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- Page 42 and 43: 42 blockwiseModulesminGap minimum c
- Page 44 and 45: 44 blockwiseModulesValueAfter all b
- Page 46 and 47: 46 checkAdjMatSourceFor references
- Page 48 and 49: 48 chooseOneHubInEachModuleDetailsV
- Page 50 and 51: 50 clusterCoefValueBoth functions o
- Page 52 and 53: 52 coClustering.permutationTestExam
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54 collapseRows# Combine cl1 and cl
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56 collapseRowshave correlation < t
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58 collapseRowsUsingKME# In this ca
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60 colQuantileCcollectGarbageIterat
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62 conformityDecompositionFactoriza
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64 conformityDecompositionis the in
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66 consensusKMEValueconsensusTOM Th
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68 consensusKMEDetailsValuerankPval
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70 consensusKMErankPvalueOptions. W
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72 consensusOrderMEsValueA datafram
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74 consensusProjectiveKMeansDetails
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76 corDetailsValueuse a character s
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78 corAndPvalue# Here the R's stand
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80 corPvalueFisherValuemeancorTestS
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82 coxRegressionResidualsDetailsVal
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84 cutreeStaticcor(datResiduals,use
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86 dynamicMergeCutArgumentscolorsco
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88 exportNetworkToVisANTValueA list
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90 fundamentalNetworkConceptsExampl
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92 GOenrichmentAnalysisUsageGOenric
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94 goodGenesinGOlogical vector with
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96 goodGenesMSgoodGenesMSFilter gen
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98 goodSamplesGenesDetailsThe const
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100 goodSamplesMSminNGenesverbosein
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102 greenWhiteRedUsagegreenBlackRed
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104 Inline display of progresshubGe
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106 intramodularConnectivity## With
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108 kMEcomparisonScatterplotkMEcomp
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110 labeledHeatmapArgumentsDetailsV
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112 labeledHeatmapxLabelsAdjxColorW
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114 labelPointsrowLabels = paste("M
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116 lowerTri2matrixDetailsValueIf l
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118 matrixToNetworkDetailsValueEach
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120 mergeCloseModulescorFnc = cor,
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122 metaAnalysisoldMEsnewMEsallOKMo
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124 metaAnalysisp.RootDoFWeightsp-v
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126 metaAnalysisIf input kruskalTes
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128 moduleEigengenesDetailsReturns
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130 moduleEigengenesDetailsValuever
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132 moduleMergeUsingKMEValueNoteMEE
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134 modulePreservationDetailsValueN
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136 modulePreservationrandomSeed se
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138 multiData.eigengeneSignificance
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140 multiSetMEseigengeneSignificanc
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142 multiSetMEsDetailsThis function
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144 mutualInfoAdjacencyDetailsValue
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146 nearestCentroidPredictordatE=da
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148 nearestCentroidPredictorassocCu
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150 nearestNeighborConnectivitypred
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152 nearestNeighborConnectivityMSne
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154 networkConceptsValueType II: co
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156 networkScreeningAuthor(s)Jun Do
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158 normalizeLabelsArgumentsdatExpr
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160 numbers2colorsSee AlsocheckSets
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162 orderBranchesUsingHubGenesValue
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164 overlapTableDetailsValuegreyLas
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166 overlapTableUsingKMEcutoffMetho
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168 pickHardThresholdmoreNetworkCon
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170 pickSoftThresholdDetailscorOpti
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172 plotClusterTreeSamplesdendroLab
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174 plotCorDetailsValueNoteIt is of
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176 plotDendroAndColorsgroupLabelsL
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178 plotEigengeneNetworkssetLabels
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180 plotMatplotMatRed and Green Col
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182 plotModuleSignificanceplotModul
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184 populationMeansInAdmixtureRefer
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186 pquantile# plot.mat(datTrueMean
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188 preservationNetworkConnectivity
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190 projectiveKMeanspairwisecomplet
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192 proportionsInAdmixtureThe stand
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194 propVarExplainedNoteThis functi
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196 qvalueDetailsIf no options are
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198 rankPvalueAuthor(s)Steve Horvat
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200 recutBlockwiseTreespValueExtrem
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202 recutBlockwiseTreesminModuleSiz
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204 recutConsensusTreesrecutConsens
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206 recutConsensusTreesDetailsValue
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208 relativeCorPredictionSuccessVal
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210 rgcolors.funcValueA matrix of r
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212 SCsListsArgumentsconnectivity v
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214 sigmoidAdjacencyFunctionValueA
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216 simulateDatExprsignumAdjacencyF
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218 simulateDatExprDetailsValuenSub
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220 simulateDatExpr5ModulesArgument
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222 simulateModulesimulateModuleSim
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224 simulateMultiExprArgumentseigen
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226 simulateSmallLayerSee Alsosimul
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228 softConnectivitysoftConnectivit
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230 standardScreeningBinaryTraitExa
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232 standardScreeningBinaryTraitSE.
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234 standardScreeningCensoredTimefa
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236 stat.bwssValueData frame with t
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238 stratifiedBarplotReferencesS. D
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240 subsetTOMSee Alsobarplot, verbo
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242 swapTwoBranchesArgumentshierTOM
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244 TOMsimilarityDetailsValueThe st
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246 TOMsimilarityFromExprArgumentsd
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248 TrueTraitcorOptions Character s
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250 unsignedAdjacencyReferencesKlem
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252 userListEnrichmentArgumentsgene
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254 userListEnrichmentprofiles in m
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256 vectorTOM# Now run the function
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258 verboseBarplotReferencesBin Zha
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260 verboseBoxplotverboseBoxplotBox
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262 verboseScatterplotablinelogical
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264 votingLinearPredictorvotingLine
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266 votingLinearPredictorNotepredic
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268 INDEXgoodGenes, 94goodGenesMS,
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270 INDEXGOenrichmentAnalysis, 91go
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272 INDEXWGCNA-package, 5