WGCNA: Weighted Correlation Network Analysis
Version 1.51

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.

Browse man pages Browse package API and functions Browse package files

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
URL http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("WGCNA")

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

AFcorMI Man page Source code
Average Source code
BloodLists Man page
BrainLists Man page
BrainRegionMarkers Man page
ClusterCoef.fun Source code
GOenrichmentAnalysis Man page Source code
GTOMdist Man page Source code
ImmunePathwayLists Man page
MAR Source code
MaxMean Source code
MinMean Source code
NPC.direct Source code
NPC.iterate Source code
PWLists Man page
SCsLists Man page
TOMdist Man page Source code
TOMplot Man page Source code
TOMsimilarity Man page Source code
TOMsimilarityFromExpr Man page Source code
TrueTrait Man page Source code
WGCNA Man page
WGCNA-package Man page
WGCNAnThreads Man page Source code
absMaxMean Source code
absMinMean Source code
accuracyMeasures Man page Source code
accuracyStatistics Source code
addErrorBars Man page Source code
addGrid Man page Source code
addGuideLines Man page Source code
addTraitToMEs Man page Source code
adjacency Man page Source code
adjacency.fromSimilarity Man page Source code
adjacency.polyReg Man page Source code
adjacency.splineReg Man page Source code
alignExpr Man page Source code
alignedFirstPC Source code
allocateJobs Man page Source code
allowWGCNAThreads Man page Source code
autoTicks Source code
automaticNetworkScreening Man page Source code
automaticNetworkScreeningGS Man page Source code
bicor Man page Source code
bicorAndPvalue Man page Source code
bicov Source code
bicovWeights Man page Source code
blockSize Man page Source code
blockwiseConsensusModules Man page Source code
blockwiseIndividualTOMs Man page Source code
blockwiseModules Man page Source code
blueWhiteRed Man page Source code
branchEigengeneDissim Man page Source code
branchSplit Man page Source code
branchSplit.dissim Man page Source code
branchSplitFromStabilityLabels Man page Source code
bucketOrder Source code
calculateIndicator Source code
causalChildren Source code
checkAdj Source code
checkAdjMat Man page Source code
checkAndDelete Source code
checkAvailableMemory Source code
checkComponents Source code
checkConsistencyOfGroupAndColID Source code
checkExpr Source code
checkSets Man page Source code
checkSimilarity Man page Source code
chooseOneHubInEachModule Man page Source code
chooseTopHubInEachModule Man page Source code
choosenew Source code
clustOrder Source code
clusterCoef Man page Source code
clusterCoeff Source code
coClustering Man page Source code
coClustering.permutationTest Man page Source code
colQuantileC Man page Source code
colWeightedMeans.x Source code
collapseRows Man page Source code
collapseRowsUsingKME Man page Source code
collectGarbage Man page Source code
collect_garbage Source code
combineAdj Source code
compiledAdjacency Source code
computeLinksInNeighbors Source code
computeSqDiagSum Source code
conformityBasedNetworkConcepts Man page Source code
conformityDecomposition Man page Source code
consensusCalculation Source code
consensusDissTOMandTree Man page Source code
consensusKME Man page Source code
consensusMEDissimilarity Man page Source code Source code
consensusOrderMEs Man page Source code
consensusProjectiveKMeans Man page Source code
consensusRepresentatives Man page Source code
consensusTOM Man page Source code
cor Man page Source code
cor1 Man page Source code
corAndPvalue Man page Source code
corFast Man page Source code
corPredictionSuccess Man page Source code
corPvalueFisher Man page Source code
corPvalueStudent Man page Source code
corWeighted Source code
corWeighted.new Source code
coreCalcForAdj Source code
coreCalcForExpr Source code
correlationPreservation Man page Source code
coxRegressionResiduals Man page Source code
cr.MaxMean Source code
cr.MinMean Source code
cr.absMaxMean Source code
cr.absMinMean Source code
cr.maxVariance Source code
cutreeStatic Man page Source code
cutreeStaticColor Man page Source code
cvPresent Source code
devianceResidual Source code
dimensions Source code
disableWGCNAThreads Man page Source code
displayColors Man page Source code
dropThirdDim Source code
dynamicMergeCut Man page Source code
empiricalBayesLM Man page Source code
emptyDist Source code
enableWGCNAThreads Man page Source code
equalizeQuantiles Source code
err.bp Source code Source code
euclideanDist.forNCP Source code
exportNetworkToCytoscape Man page Source code
exportNetworkToVisANT Man page Source code
extend Source code
filterSimilarPS Source code
fixDataStructure Man page Source code
formatLabels Man page Source code
fundamentalNetworkConcepts Man page Source code
getBranchMembers Source code
getSVDs Source code
goodGenes Man page Source code
goodGenesMS Man page Source code
goodSamples Man page Source code
goodSamplesGenes Man page Source code
goodSamplesGenesMS Man page Source code
goodSamplesMS Man page Source code
greenBlackRed Man page Source code
greenWhiteRed Man page Source code
heatmap Source code
heatmapWithLegend Source code
histogramsWithCommonBreaks Source code
hubGeneSignificance Man page Source code
initProgInd Man page Source code
intramodularConnectivity Man page Source code
intramodularConnectivity.fromExpr Man page Source code
isMultiData Man page Source code
kIM Source code
kMEcomparisonScatterplot Man page Source code
keepCommonProbes Man page Source code
labelPoints Man page Source code
labeledBarplot Man page Source code
labeledHeatmap Man page Source code
labeledHeatmap.multiPage Man page Source code
labels2colors Man page Source code
list2multiData Man page Source code
listRep Source code
loadObject Source code
lowerTri2matrix Man page Source code
matchLabels Man page Source code
matrixToNetwork Man page Source code
maxRowVariance Source code
meanInRange Source code
mergeCloseModules Man page Source code
metaAnalysis Man page Source code
metaZfunction Man page Source code
minTreeHeight Source code
moduleColor.getMEprefix Man page Source code
moduleEigengenes Man page Source code
moduleMergeUsingKME Man page Source code
moduleNumber Man page Source code
modulePreservation Man page Source code
modulePreservationInternal Source code
mtd.apply Man page Source code
mtd.applyToSubset Man page Source code
mtd.branchEigengeneDissim Man page Source code
mtd.colnames Man page Source code
mtd.mapply Man page Source code
mtd.rbindSelf Man page Source code
mtd.setAttr Man page Source code
mtd.setColnames Man page Source code
mtd.simplify Man page Source code
mtd.subset Man page Source code
multiData Man page Source code
multiData.eigengeneSignificance Man page Source code
multiData2list Man page Source code
multiIntersect Man page Source code
multiSetMEs Man page Source code
multiUnion Man page Source code
mutualInfoAdjacency Man page Source code
nNAColors Source code
nPresent Man page Source code
nProcessorsOnline Source code
nSets Man page Source code
nearestCentroidPredictor Man page Source code
nearestNeighborConnectivity Man page Source code
nearestNeighborConnectivityMS Man page Source code
networkConcepts Man page Source code
networkScreening Man page Source code
networkScreeningGS Man page Source code
normalizeLabels Man page Source code
nterleave Source code
numbers2colors Man page Source code
offDiagonalMatrixSum Source code
onAttach Source code
orderBranchesUsingHubGenes Man page Source code
orderLabelsBySize Source code
orderMEs Man page Source code
overlapTable Man page Source code
overlapTableUsingKME Man page Source code
pValueFromZ Source code
panel.cor Source code
panel.hist Source code
permissiveDim Source code
phyper2 Source code
pickHardThreshold Man page Source code
pickHardThreshold.fromSimilarity Man page Source code
pickSoftThreshold Man page Source code
pickSoftThreshold.fromSimilarity Man page Source code
plotClusterTreeSamples Man page Source code
plotColorLegend Source code
plotColorUnderTree Man page Source code
plotCor Man page Source code
plotDendroAndColors Man page Source code
plotDendrogram Source code
plotEigengeneNetworks Man page Source code
plotMEpairs Man page Source code
plotMat Man page Source code
plotModuleSignificance Man page Source code
plotNetworkHeatmap Man page Source code
plotOrderedColors Man page Source code
pmean Man page Source code
pmedian Man page Source code
populationMeansInAdmixture Man page Source code
pquantile Man page Source code
prepComma Man page Source code
prependZeros Man page Source code
preservationNetworkConnectivity Man page Source code
processFileName Source code
projectiveKMeans Man page Source code
propVarExplained Man page Source code
proportionsInAdmixture Man page Source code
qValueFromP Source code
qorder Source code
quickGeneVotingPredictor Source code
quickGeneVotingPredictor.CV Source code
qvalue Man page Source code
qvalue.restricted Man page Source code
randIndex Man page Source code
rankPvalue Man page Source code
recutBlockwiseTrees Man page Source code
recutConsensusTrees Man page Source code
redWhiteGreen Man page Source code
reflectBranch Man page Source code
relativeCorPredictionSuccess Man page Source code
removeGreyME Man page Source code
removePrincipalComponents Man page Source code
returnGeneSetsAsList Man page Source code
reverseRows Source code
reverseVector Source code
rgcolors.func Man page Source code
rowQuantileC Man page Source code
s.adjmat Source code
sBinary Source code
saveChunks Source code
scaleFreeFitIndex Man page Source code
scaleFreePlot Man page Source code
selectBranch Man page Source code
selectFewestConsensusMissing Man page Source code
selectFewestMissing Source code
setCorrelationPreservation Man page Source code
shiftList Source code
shortenStrings Man page Source code
sigmoidAdjacencyFunction Man page Source code
signedKME Man page Source code
signumAdjacencyFunction Man page Source code
simulateDatExpr Man page Source code
simulateDatExpr5Modules Man page Source code
simulateEigengeneNetwork Man page Source code
simulateModule Man page Source code
simulateMultiExpr Man page Source code
simulateSmallLayer Man page Source code
sizeDependentQuantile Source code
sizeGrWindow Man page Source code
softConnectivity Man page Source code
softConnectivity.fromSimilarity Man page Source code
spaste Man page Source code
standardColors Man page Source code
standardScreeningBinaryTrait Man page Source code
standardScreeningCensoredTime Man page Source code
standardScreeningNumericTrait Man page Source code
stdErr Man page Source code
stratifiedBarplot Man page Source code
subsetTOM Man page Source code
substituteTags Source code
swapTwoBranches Man page Source code
table2.allLevels Source code
tableOrd Source code
transposeBigData Man page Source code
turnDistVectorIntoMatrix Source code
turnVectorIntoDist Source code
unsignedAdjacency Man page Source code
updateProgInd Man page Source code
useNThreads Source code
userListEnrichment Man page Source code
vector2dist Source code
vectorTOM Man page Source code
vectorizeMatrix Man page Source code
verboseBarplot Man page Source code
verboseBoxplot Man page Source code
verboseIplot Man page Source code
verboseScatterplot Man page Source code
votingLinearPredictor Man page Source code
weightedScale Source code
weightedVar Source code

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
WGCNA documentation built on May 20, 2017, 5:17 a.m.