WGCNA: Weighted Correlation Network Analysis

Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.

Install the latest version of this package by entering the following in R:
install.packages("WGCNA")
AuthorPeter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Date of publication2016-03-15 00:24:08
MaintainerPeter Langfelder <Peter.Langfelder@gmail.com>
LicenseGPL (>= 2)
Version1.51
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/

View on CRAN

Man pages

accuracyMeasures: Accuracy measures for a 2x2 confusion matrix or for vectors...

addErrorBars: Add error bars to a barplot.

addGrid: Add grid lines to an existing plot.

addGuideLines: Add vertical "guide lines" to a dendrogram plot

addTraitToMEs: Add trait information to multi-set module eigengene structure

adjacency: Calculate network adjacency

adjacency.polyReg: Adjacency matrix based on polynomial regression

adjacency.splineReg: Calculate network adjacency based on natural cubic spline...

AFcorMI: Prediction of Weighted Mutual Information Adjacency Matrix by...

alignExpr: Align expression data with given vector

allocateJobs: Divide tasks among workers

allowWGCNAThreads: Allow and disable multi-threading for certain WGCNA...

automaticNetworkScreening: One-step automatic network gene screening

automaticNetworkScreeningGS: One-step automatic network gene screening with external gene...

bicor: Biweight Midcorrelation

bicorAndPvalue: Calculation of biweight midcorrelations and associated...

bicovWeights: Weights used in biweight midcovariance

blockSize: Attempt to calculate an appropriate block size to maximize...

blockwiseConsensusModules: Find consensus modules across several datasets.

blockwiseIndividualTOMs: Calculation of block-wise topological overlaps

blockwiseModules: Automatic network construction and module detection

BloodLists: Blood Cell Types with Corresponding Gene Markers

blueWhiteRed: Blue-white-red color sequence

BrainLists: Brain-Related Categories with Corresponding Gene Markers

BrainRegionMarkers: Gene Markers for Regions of the Human Brain

branchEigengeneDissim: Branch dissimilarity based on eigennodes (eigengenes).

branchSplit: Branch split.

branchSplit.dissim: Branch split based on dissimilarity.

branchSplitFromStabilityLabels: Branch split (dissimilarity) statistic derived from labels...

checkAdjMat: Check adjacency matrix

checkSets: Check structure and retrieve sizes of a group of datasets.

chooseOneHubInEachModule: Chooses a single hub gene in each module

chooseTopHubInEachModule: Chooses the top hub gene in each module

clusterCoef: Clustering coefficient calculation

coClustering: Co-clustering measure of cluster preservation between two...

coClustering.permutationTest: Permutation test for co-clustering

collapseRows: Select one representative row per group

collapseRowsUsingKME: Selects one representative row per group based on kME

collectGarbage: Iterative garbage collection.

colQuantileC: Fast colunm- and row-wise quantile of a matrix.

conformityBasedNetworkConcepts: Calculation of conformity-based network concepts.

conformityDecomposition: Conformity and module based decomposition of a network...

consensusDissTOMandTree: Consensus clustering based on topological overlap and...

consensusKME: Calculate consensus kME (eigengene-based connectivities)...

consensusMEDissimilarity: Consensus dissimilarity of module eigengenes.

consensusOrderMEs: Put close eigenvectors next to each other in several sets.

consensusProjectiveKMeans: Consensus projective K-means (pre-)clustering of expression...

consensusRepresentatives: Consensus selection of group representatives

consensusTOM: Consensus network (topological overlap).

cor: Fast calculations of Pearson correlation.

corAndPvalue: Calculation of correlations and associated p-values

corPredictionSuccess: Qunatification of success of gene screening

corPvalueFisher: Fisher's asymptotic p-value for correlation

corPvalueStudent: Student asymptotic p-value for correlation

correlationPreservation: Preservation of eigengene correlations

coxRegressionResiduals: Deviance- and martingale residuals from a Cox regression...

cutreeStatic: Constant-height tree cut

cutreeStaticColor: Constant height tree cut using color labels

displayColors: Show colors used to label modules

dynamicMergeCut: Threshold for module merging

empiricalBayesLM: Empirical Bayes-moderated adjustment for unwanted covariates

exportNetworkToCytoscape: Export network to Cytoscape

exportNetworkToVisANT: Export network data in format readable by VisANT

fixDataStructure: Put single-set data into a form useful for multiset...

formatLabels: Break long character strings into multiple lines

fundamentalNetworkConcepts: Calculation of fundamental network concepts from an adjacency...

GOenrichmentAnalysis: Calculation of GO enrichment (experimental)

goodGenes: Filter genes with too many missing entries

goodGenesMS: Filter genes with too many missing entries across multiple...

goodSamples: Filter samples with too many missing entries

goodSamplesGenes: Iterative filtering of samples and genes with too many...

goodSamplesGenesMS: Iterative filtering of samples and genes with too many...

goodSamplesMS: Filter samples with too many missing entries across multiple...

greenBlackRed: Green-black-red color sequence

greenWhiteRed: Green-white-red color sequence

GTOMdist: Generalized Topological Overlap Measure

hubGeneSignificance: Hubgene significance

ImmunePathwayLists: Immune Pathways with Corresponding Gene Markers

initProgInd: Inline display of progress

intramodularConnectivity: Calculation of intramodular connectivity

isMultiData: Determine whether the supplied object is a valid multiData...

keepCommonProbes: Keep probes that are shared among given data sets

kMEcomparisonScatterplot: Function to plot kME values between two comparable data sets.

labeledBarplot: Barplot with text or color labels.

labeledHeatmap: Produce a labeled heatmap plot

labeledHeatmap.multiPage: Labeled heatmap divided into several separate plots.

labelPoints: Label scatterplot points

labels2colors: Convert numerical labels to colors.

list2multiData: Convert a list to a multiData structure and vice-versa.

lowerTri2matrix: Reconstruct a symmetric matrix from a distance...

matchLabels: Relabel module labels to best match the given reference...

matrixToNetwork: Construct a network from a matrix

mergeCloseModules: Merge close modules in gene expression data

metaAnalysis: Meta-analysis of binary and continuous variables

metaZfunction: Meta-analysis Z statistic

moduleColor.getMEprefix: Get the prefix used to label module eigengenes.

moduleEigengenes: Calculate module eigengenes.

moduleMergeUsingKME: Merge modules and reassign genes using kME.

moduleNumber: Fixed-height cut of a dendrogram.

modulePreservation: Calculation of module preservation statistics

mtd.apply: Apply a function to each set in a multiData structure.

mtd.mapply: Apply a function to elements of given multiData structures.

mtd.rbindSelf: Turn a multiData structure into a single matrix or data...

mtd.setAttr: Set attributes on each component of a multiData structure

mtd.setColnames: Get and set column names in a multiData structure.

mtd.simplify: If possible, simplify a multiData structure to a...

mtd.subset: Subset rows and columns in a multiData structure

multiData: Create a multiData structure.

multiData.eigengeneSignificance: Eigengene significance across multiple sets

multiSetMEs: Calculate module eigengenes.

multiUnion: Union and intersection of multiple sets

mutualInfoAdjacency: Calculate weighted adjacency matrices based on mutual...

nearestCentroidPredictor: Nearest centroid predictor

nearestNeighborConnectivity: Connectivity to a constant number of nearest neighbors

nearestNeighborConnectivityMS: Connectivity to a constant number of nearest neighbors across...

networkConcepts: Calculations of network concepts

networkScreening: Identification of genes related to a trait

networkScreeningGS: Network gene screening with an external gene significance...

normalizeLabels: Transform numerical labels into normal order.

nPresent: Number of present data entries.

nSets: Number of sets in a multi-set variable

numbers2colors: Color representation for a numeric variable

orderBranchesUsingHubGenes: Optimize dendrogram using branch swaps and reflections.

orderMEs: Put close eigenvectors next to each other

overlapTable: Calculate overlap of modules

overlapTableUsingKME: Determines significant overlap between modules in two...

pickHardThreshold: Analysis of scale free topology for hard-thresholding.

pickSoftThreshold: Analysis of scale free topology for soft-thresholding

plotClusterTreeSamples: Annotated clustering dendrogram of microarray samples

plotColorUnderTree: Plot color rows in a given order, for example under a...

plotCor: Red and Green Color Image of Correlation Matrix

plotDendroAndColors: Dendrogram plot with color annotation of objects

plotEigengeneNetworks: Eigengene network plot

plotMat: Red and Green Color Image of Data Matrix

plotMEpairs: Pairwise scatterplots of eigengenes

plotModuleSignificance: Barplot of module significance

plotNetworkHeatmap: Network heatmap plot

populationMeansInAdmixture: Estimate the population-specific mean values in an admixed...

pquantile: Parallel quantile, median, mean

prepComma: Prepend a comma to a non-empty string

prependZeros: Pad numbers with leading zeros to specified total width

preservationNetworkConnectivity: Network preservation calculations

projectiveKMeans: Projective K-means (pre-)clustering of expression data

proportionsInAdmixture: Estimate the proportion of pure populations in an admixed...

propVarExplained: Proportion of variance explained by eigengenes.

PWLists: Pathways with Corresponding Gene Markers - Compiled by Mike...

qvalue: Estimate the q-values for a given set of p-values

qvalue.restricted: qvalue convenience wrapper

randIndex: Rand index of two partitions

rankPvalue: Estimate the p-value for ranking consistently high (or low)...

recutBlockwiseTrees: Repeat blockwise module detection from pre-calculated data

recutConsensusTrees: Repeat blockwise consensus module detection from...

redWhiteGreen: Red-white-green color sequence

relativeCorPredictionSuccess: Compare prediction success

removeGreyME: Removes the grey eigengene from a given collection of...

removePrincipalComponents: Remove leading principal components from data

returnGeneSetsAsList: Return pre-defined gene lists in several biomedical...

rgcolors.func: Red and Green Color Specification

scaleFreeFitIndex: Calculation of fitting statistics for evaluating scale free...

scaleFreePlot: Visual check of scale-free topology

SCsLists: Stem Cell-Related Genes with Corresponding Gene Markers

selectFewestConsensusMissing: Select columns with the lowest consensus number of missing...

setCorrelationPreservation: Summary correlation preservation measure

shortenStrings: Shorten given character strings by truncating at a suitable...

sigmoidAdjacencyFunction: Sigmoid-type adacency function.

signedKME: Signed eigengene-based connectivity

signumAdjacencyFunction: Hard-thresholding adjacency function

simulateDatExpr: Simulation of expression data

simulateDatExpr5Modules: Simplified simulation of expression data

simulateEigengeneNetwork: Simulate eigengene network from a causal model

simulateModule: Simulate a gene co-expression module

simulateMultiExpr: Simulate multi-set expression data

simulateSmallLayer: Simulate small modules

sizeGrWindow: Opens a graphics window with specified dimensions

softConnectivity: Calculates connectivity of a weighted network.

spaste: Space-less paste

standardColors: Colors this library uses for labeling modules.

standardScreeningBinaryTrait: Standard screening for binatry traits

standardScreeningCensoredTime: Standard Screening with regard to a Censored Time Variable

standardScreeningNumericTrait: Standard screening for numeric traits

stdErr: Standard error of the mean of a given vector.

stratifiedBarplot: Bar plots of data across two splitting parameters

subsetTOM: Topological overlap for a subset of a whole set of genes

swapTwoBranches: Select, swap, or reflect branches in a dendrogram.

TOMplot: Graphical representation of the Topological Overlap Matrix

TOMsimilarity: Topological overlap matrix similarity and dissimilarity

TOMsimilarityFromExpr: Topological overlap matrix

transposeBigData: Transpose a big matrix or data frame

TrueTrait: Estimate the true trait underlying a list of surrogate...

unsignedAdjacency: Calculation of unsigned adjacency

userListEnrichment: Measure enrichment between inputted and user-defined lists

vectorizeMatrix: Turn a matrix into a vector of non-redundant components

vectorTOM: Topological overlap for a subset of the whole set of genes

verboseBarplot: Barplot with error bars, annotated by Kruskal-Wallis or ANOVA...

verboseBoxplot: Boxplot annotated by a Kruskal-Wallis p-value

verboseIplot: Scatterplot with density

verboseScatterplot: Scatterplot annotated by regression line and p-value

votingLinearPredictor: Voting linear predictor

WGCNA-package: Weighted Gene Co-Expression Network Analysis

Functions

accuracyMeasures Man page
addErrorBars Man page
addGrid Man page
addGuideLines Man page
addTraitToMEs Man page
adjacency Man page
adjacency.fromSimilarity Man page
adjacency.polyReg Man page
adjacency.splineReg Man page
AFcorMI Man page
alignExpr Man page
allocateJobs Man page
allowWGCNAThreads Man page
automaticNetworkScreening Man page
automaticNetworkScreeningGS Man page
bicor Man page
bicorAndPvalue Man page
bicovWeights Man page
blockSize Man page
blockwiseConsensusModules Man page
blockwiseIndividualTOMs Man page
blockwiseModules Man page
BloodLists Man page
blueWhiteRed Man page
BrainLists Man page
BrainRegionMarkers Man page
branchEigengeneDissim Man page
branchSplit Man page
branchSplit.dissim Man page
branchSplitFromStabilityLabels Man page
checkAdjMat Man page
checkSets Man page
checkSimilarity Man page
chooseOneHubInEachModule Man page
chooseTopHubInEachModule Man page
clusterCoef Man page
coClustering Man page
coClustering.permutationTest Man page
collapseRows Man page
collapseRowsUsingKME Man page
collectGarbage Man page
colQuantileC Man page
conformityBasedNetworkConcepts Man page
conformityDecomposition Man page
consensusDissTOMandTree Man page
consensusKME Man page
consensusMEDissimilarity Man page
consensusOrderMEs Man page
consensusProjectiveKMeans Man page
consensusRepresentatives Man page
consensusTOM Man page
cor Man page
cor1 Man page
corAndPvalue Man page
corFast Man page
corPredictionSuccess Man page
corPvalueFisher Man page
corPvalueStudent Man page
correlationPreservation Man page
coxRegressionResiduals Man page
cutreeStatic Man page
cutreeStaticColor Man page
disableWGCNAThreads Man page
displayColors Man page
dynamicMergeCut Man page
empiricalBayesLM Man page
enableWGCNAThreads Man page
exportNetworkToCytoscape Man page
exportNetworkToVisANT Man page
fixDataStructure Man page
formatLabels Man page
fundamentalNetworkConcepts Man page
GOenrichmentAnalysis Man page
goodGenes Man page
goodGenesMS Man page
goodSamples Man page
goodSamplesGenes Man page
goodSamplesGenesMS Man page
goodSamplesMS Man page
greenBlackRed Man page
greenWhiteRed Man page
GTOMdist Man page
hubGeneSignificance Man page
ImmunePathwayLists Man page
initProgInd Man page
intramodularConnectivity Man page
intramodularConnectivity.fromExpr Man page
isMultiData Man page
keepCommonProbes Man page
kMEcomparisonScatterplot Man page
labeledBarplot Man page
labeledHeatmap Man page
labeledHeatmap.multiPage Man page
labelPoints Man page
labels2colors Man page
list2multiData Man page
lowerTri2matrix Man page
matchLabels Man page
matrixToNetwork Man page
mergeCloseModules Man page
metaAnalysis Man page
metaZfunction Man page
moduleColor.getMEprefix Man page
moduleEigengenes Man page
moduleMergeUsingKME Man page
moduleNumber Man page
modulePreservation Man page
mtd.apply Man page
mtd.applyToSubset Man page
mtd.branchEigengeneDissim Man page
mtd.colnames Man page
mtd.mapply Man page
mtd.rbindSelf Man page
mtd.setAttr Man page
mtd.setColnames Man page
mtd.simplify Man page
mtd.subset Man page
multiData Man page
multiData2list Man page
multiData.eigengeneSignificance Man page
multiIntersect Man page
multiSetMEs Man page
multiUnion Man page
mutualInfoAdjacency Man page
nearestCentroidPredictor Man page
nearestNeighborConnectivity Man page
nearestNeighborConnectivityMS Man page
networkConcepts Man page
networkScreening Man page
networkScreeningGS Man page
normalizeLabels Man page
nPresent Man page
nSets Man page
numbers2colors Man page
orderBranchesUsingHubGenes Man page
orderMEs Man page
overlapTable Man page
overlapTableUsingKME Man page
pickHardThreshold Man page
pickHardThreshold.fromSimilarity Man page
pickSoftThreshold Man page
pickSoftThreshold.fromSimilarity Man page
plotClusterTreeSamples Man page
plotColorUnderTree Man page
plotCor Man page
plotDendroAndColors Man page
plotEigengeneNetworks Man page
plotMat Man page
plotMEpairs Man page
plotModuleSignificance Man page
plotNetworkHeatmap Man page
plotOrderedColors Man page
pmean Man page
pmedian Man page
populationMeansInAdmixture Man page
pquantile Man page
prepComma Man page
prependZeros Man page
preservationNetworkConnectivity Man page
projectiveKMeans Man page
proportionsInAdmixture Man page
propVarExplained Man page
PWLists Man page
qvalue Man page
qvalue.restricted Man page
randIndex Man page
rankPvalue Man page
recutBlockwiseTrees Man page
recutConsensusTrees Man page
redWhiteGreen Man page
reflectBranch Man page
relativeCorPredictionSuccess Man page
removeGreyME Man page
removePrincipalComponents Man page
returnGeneSetsAsList Man page
rgcolors.func Man page
rowQuantileC Man page
scaleFreeFitIndex Man page
scaleFreePlot Man page
SCsLists Man page
selectBranch Man page
selectFewestConsensusMissing Man page
setCorrelationPreservation Man page
shortenStrings Man page
sigmoidAdjacencyFunction Man page
signedKME Man page
signumAdjacencyFunction Man page
simulateDatExpr Man page
simulateDatExpr5Modules Man page
simulateEigengeneNetwork Man page
simulateModule Man page
simulateMultiExpr Man page
simulateSmallLayer Man page
sizeGrWindow Man page
softConnectivity Man page
softConnectivity.fromSimilarity Man page
spaste Man page
standardColors Man page
standardScreeningBinaryTrait Man page
standardScreeningCensoredTime Man page
standardScreeningNumericTrait Man page
stdErr Man page
stratifiedBarplot Man page
subsetTOM Man page
swapTwoBranches Man page
TOMdist Man page
TOMplot Man page
TOMsimilarity Man page
TOMsimilarityFromExpr Man page
transposeBigData Man page
TrueTrait Man page
unsignedAdjacency Man page
updateProgInd Man page
userListEnrichment Man page
vectorizeMatrix Man page
vectorTOM Man page
verboseBarplot Man page
verboseBoxplot Man page
verboseIplot Man page
verboseScatterplot Man page
votingLinearPredictor Man page
WGCNA Man page
WGCNAnThreads Man page
WGCNA-package Man page

Files

inst
inst/CITATION
src
src/pivot.h
src/quantileC.cc
src/Makevars
src/compiling.h
src/corFunctions-common.h
src/array.h
src/bucketApproxSort.cc
src/corFunctions-unified.c
src/corFunctions-common.c
src/corFunctions.h
src/pivot.c
src/networkFunctions.c
src/exceptions.h
src/Makevars.win
src/arrayGeneric.h
NAMESPACE
data
data/BrainRegionMarkers.rda
data/BrainLists.rda
data/BloodLists.rda
data/PWLists.rda
data/ImmunePathwayLists.rda
data/SCsLists.rda
Changelog
R
R/adjacency.polyReg.R R/networkConcepts.R R/stratifiedBarplot.R R/modulePreservation.R R/Functions.R R/GOenrichmentAnalysis.R R/verboseIplot.R R/adjacency.splineReg.R R/standardScreeningBinaryTrait.R R/corAndPvalue.R R/consensusTOM.R R/qvalue.R R/nearestCentroidPredictor.R R/heatmapWithLegend.R R/matchLabels.R R/labelPoints.R R/dendrogramAdjustmentFunctions.R R/votingLinearPredictor.R R/branchSplit.R R/returnGeneSetsAsList.R R/proportionsInAdmixture.R R/TrueTrait.R R/overlapTableUsingKME.R R/userListEnrichment.R R/transposeBigData.R R/plotDendrogram.R R/kMEcomparisonScatterplot.R R/collapseRows.R R/Functions-fromSimilarity.R R/populationMeansInAdmixture.R R/AFcorMI.R R/blockwiseModulesC.R R/pquantile.R R/consensusDissTOMandTree.R R/moduleMergeUsingKME.R R/empiricalBayesLM.R R/mutualInfoAdjacency.R R/smaFunctions.R R/coxRegressionResiduals.R R/quantileC.R R/collapseRowsUsingKME.R R/exportFunctions.R R/bucketOrder.R R/internalConstants.R R/useNThreads.R R/consensusRepresentatives.R R/coClustering.R R/multiData.R R/conformityDecomposition.R R/corFunctions.R R/Functions-multiData.R R/zzz.R R/accuracyMeasures.R
MD5
DESCRIPTION
man
man/corPredictionSuccess.Rd man/allowWGCNAThreads.Rd man/TrueTrait.Rd man/transposeBigData.Rd man/removeGreyME.Rd man/mtd.setColnames.Rd man/accuracyMeasures.Rd man/plotMat.Rd man/signumAdjacencyFunction.Rd man/adjacency.Rd man/sigmoidAdjacencyFunction.Rd man/nearestCentroidPredictor.Rd man/projectiveKMeans.Rd man/conformityBasedNetworkConcepts.Rd man/overlapTable.Rd man/bicorAndPvalue.Rd man/chooseTopHubInEachModule.Rd man/blueWhiteRed.Rd man/consensusOrderMEs.Rd man/branchSplitFromStabilityLabels.Rd man/orderMEs.Rd man/mtd.mapply.Rd man/collectGarbage.Rd man/networkScreeningGS.Rd man/WGCNA-package.Rd man/orderBranchesUsingHubGenes.Rd man/multiUnion.Rd man/sizeGrWindow.Rd man/normalizeLabels.Rd man/GOenrichmentAnalysis.Rd man/labeledHeatmap.Rd man/goodSamples.Rd man/scaleFreeFitIndex.Rd man/goodSamplesGenes.Rd man/isMultiData.Rd man/plotCor.Rd man/empiricalBayesLM.Rd man/consensusKME.Rd man/plotModuleSignificance.Rd man/chooseOneHubInEachModule.Rd man/multiData.eigengeneSignificance.Rd man/consensusProjectiveKMeans.Rd man/nearestNeighborConnectivity.Rd man/automaticNetworkScreening.Rd man/TOMsimilarityFromExpr.Rd man/standardScreeningBinaryTrait.Rd man/checkAdjMat.Rd man/cutreeStatic.Rd man/rankPvalue.Rd man/exportNetworkToCytoscape.Rd man/subsetTOM.Rd man/kMEcomparisonScatterplot.Rd man/metaZfunction.Rd man/bicor.Rd man/ImmunePathwayLists.Rd man/collapseRows.Rd man/simulateSmallLayer.Rd man/cor.Rd man/prependZeros.Rd man/networkConcepts.Rd man/corAndPvalue.Rd man/goodSamplesGenesMS.Rd man/blockSize.Rd man/coxRegressionResiduals.Rd man/addTraitToMEs.Rd man/standardScreeningNumericTrait.Rd man/simulateDatExpr5Modules.Rd man/plotEigengeneNetworks.Rd man/branchSplit.Rd man/populationMeansInAdmixture.Rd man/mtd.rbindSelf.Rd man/matrixToNetwork.Rd man/mtd.subset.Rd man/pickSoftThreshold.Rd man/selectFewestConsensusMissing.Rd man/lowerTri2matrix.Rd man/moduleColor.getMEprefix.Rd man/plotClusterTreeSamples.Rd man/labelPoints.Rd man/bicovWeights.Rd man/corPvalueStudent.Rd man/automaticNetworkScreeningGS.Rd man/mtd.setAttr.Rd man/addGuideLines.Rd man/vectorizeMatrix.Rd man/fixDataStructure.Rd man/signedKME.Rd man/consensusRepresentatives.Rd man/TOMsimilarity.Rd man/labeledHeatmap.multiPage.Rd man/dynamicMergeCut.Rd man/alignExpr.Rd man/consensusTOM.Rd man/returnGeneSetsAsList.Rd man/mergeCloseModules.Rd man/verboseScatterplot.Rd man/colQuantileC.Rd man/numbers2colors.Rd man/coClustering.permutationTest.Rd man/multiData.Rd man/labels2colors.Rd man/nearestNeighborConnectivityMS.Rd man/consensusMEDissimilarity.Rd man/nSets.Rd man/matchLabels.Rd man/SCsLists.Rd man/simulateDatExpr.Rd man/standardScreeningCensoredTime.Rd man/greenWhiteRed.Rd man/collapseRowsUsingKME.Rd man/blockwiseConsensusModules.Rd man/exportNetworkToVisANT.Rd man/stdErr.Rd man/TOMplot.Rd man/allocateJobs.Rd man/BrainRegionMarkers.Rd man/removePrincipalComponents.Rd man/redWhiteGreen.Rd man/coClustering.Rd man/simulateMultiExpr.Rd man/prepComma.Rd man/rgcolors.func.Rd man/intramodularConnectivity.Rd man/moduleEigengenes.Rd man/goodSamplesMS.Rd man/setCorrelationPreservation.Rd man/plotNetworkHeatmap.Rd man/blockwiseIndividualTOMs.Rd man/propVarExplained.Rd man/BrainLists.Rd man/checkSets.Rd man/addErrorBars.Rd man/goodGenesMS.Rd man/relativeCorPredictionSuccess.Rd man/qvalue.Rd man/scaleFreePlot.Rd man/nPresent.Rd man/preservationNetworkConnectivity.Rd man/spaste.Rd man/verboseBoxplot.Rd man/keepCommonProbes.Rd man/conformityDecomposition.Rd man/standardColors.Rd man/proportionsInAdmixture.Rd man/cutreeStaticColor.Rd man/labeledBarplot.Rd man/overlapTableUsingKME.Rd man/multiSetMEs.Rd man/hubGeneSignificance.Rd man/mutualInfoAdjacency.Rd man/pquantile.Rd man/shortenStrings.Rd man/simulateEigengeneNetwork.Rd man/verboseIplot.Rd man/simulateModule.Rd man/addGrid.Rd man/greenBlackRed.Rd man/softConnectivity.Rd man/clusterCoef.Rd man/branchSplit.dissim.Rd man/qvalue.restricted.Rd man/pickHardThreshold.Rd man/initProgInd.Rd man/recutBlockwiseTrees.Rd man/formatLabels.Rd man/networkScreening.Rd man/corPvalueFisher.Rd man/mtd.simplify.Rd man/goodGenes.Rd man/vectorTOM.Rd man/adjacency.polyReg.Rd man/adjacency.splineReg.Rd man/modulePreservation.Rd man/swapTwoBranches.Rd man/consensusDissTOMandTree.Rd man/BloodLists.Rd man/plotDendroAndColors.Rd man/plotColorUnderTree.Rd man/metaAnalysis.Rd man/plotMEpairs.Rd man/verboseBarplot.Rd man/stratifiedBarplot.Rd man/GTOMdist.Rd man/fundamentalNetworkConcepts.Rd man/blockwiseModules.Rd man/correlationPreservation.Rd man/list2multiData.Rd man/userListEnrichment.Rd man/recutConsensusTrees.Rd man/mtd.apply.Rd man/votingLinearPredictor.Rd man/displayColors.Rd man/unsignedAdjacency.Rd man/AFcorMI.Rd man/moduleNumber.Rd man/moduleMergeUsingKME.Rd man/branchEigengeneDissim.Rd man/randIndex.Rd man/PWLists.Rd

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