API for WGCNA
Weighted Correlation Network Analysis

Global functions
AFcorMI Man page Source code
Average Source code
BD.actualFileNames Man page Source code
BD.blockLengths Man page Source code
BD.checkAndDeleteFiles Man page Source code
BD.getData Man page Source code
BD.getMetaData Man page Source code
BD.nBlocks Man page Source code
BlockInformation Man page
BlockwiseData Man page
BloodLists Man page
BrainLists Man page
BrainRegionMarkers Man page
ClusterCoef.fun Source code
ConsensusOptions Man page
ConsensusTree Man page
CorrelationOptions Man page
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
NetworkOptions Man page
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
addBlockToBlockwiseData Man page Source code
addErrorBars Man page Source code
addErrorBars.2sided 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
bicovWeightFactors Man page Source code
bicovWeights Man page Source code
bicovWeightsFromFactors 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
branchEigengeneSimilarity Man page Source code
branchSplit Man page Source code
branchSplit.dissim Man page Source code
branchSplitFromStabilityLabels Man page Source code
branchSplitFromStabilityLabels.individualFraction Man page Source code
branchSplitFromStabilityLabels.prediction Man page Source code
calculateIndicator Source code
causalChildren Source code
checkAdj Source code
checkAdjMat Man page Source code
checkAndDelete Source code
checkAndScaleMultiWeights Source code
checkAndScaleWeights Source code
checkAvailableMemory Source code
checkComponents Source code
checkConsistencyOfGroupAndColID Source code
checkExpr Source code
checkListDimConsistencyAndGetDimnames Source code
checkListNamesConsistency Source code
checkLogicalConsistency Source code
checkPower 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
colWeightedVars Source code
collapseRows Man page Source code
collapseRowsUsingKME Man page Source code
collectGarbage Man page Source code
collect_garbage Source code
combineAdj Source code
computeLinksInNeighbors Source code
computeSqDiagSum Source code
conformityBasedNetworkConcepts Man page Source code
conformityDecomposition Man page Source code
consensusCalculation Man page Source code
consensusCalculation.base Source code
consensusCalculation.base.FromList 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
corCalculation 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
effectiveNChar 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
getAttributesOrEmptyList Source code
getBranchMembers Source code
getData Source code
getElement 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
hierarchicalBranchEigengeneDissim Man page Source code
hierarchicalConsensusCalculation Man page Source code
hierarchicalConsensusKME Man page Source code
hierarchicalConsensusMEDissimilarity Man page Source code Source code
hierarchicalConsensusModules Man page Source code
hierarchicalConsensusTOM Man page Source code
hierarchicalMergeCloseModules Man page Source code
histogramsWithCommonBreaks Source code
hubGeneSignificance Man page Source code
imputeByModule Man page Source code
individualTOMs 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
linearModelCoefficients Source code
list2multiData Man page Source code
listRep Source code
loadAsList 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
mergeBlockwiseData Man page Source code
mergeCloseModules Man page Source code
mergeConsensusTOMInformationLists Source code
metaAnalysis Man page Source code
metaZfunction Man page Source code
minTreeHeight Source code
minWhichMin Man page 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.checkDimConsistencyAndGetDimnames 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
multiGSub Man page Source code
multiGrep Man page Source code
multiGrepl Man page Source code
multiIntersect Man page Source code
multiPlot Source code
multiSetMEs Man page Source code
multiSub 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
networkCalculation Source code
networkConcepts Man page Source code
networkScreening Man page Source code
networkScreeningGS Man page Source code
newBlockInformation Man page Source code
newBlockwiseData Man page Source code
newConsensusOptions Man page Source code
newConsensusTree Man page Source code
newCorrelationOptions Man page Source code
newNetworkOptions Man page Source code
nitialFit.defaultOptions Source code
nitialFit.defaultWeightName Source code
nitialFit.requiresFormula 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
orderMEsByHierarchicalConsensus 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
plotMultiHist Man page Source code
plotNetworkHeatmap Man page Source code
plotOrderedColors Man page Source code
plotStandaloneLegend Source code
pmean Man page Source code
pmean.fromList Man page Source code
pmedian Man page Source code
pminWhich.fromList Man page Source code
populationMeansInAdmixture Man page Source code
pquantile Man page Source code
pquantile.fromList 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
pruneAndMergeConsensusModules Man page Source code
pruneConsensusModules 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
replaceMissing 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
sampledBlockwiseModules Man page Source code
sampledHierarchicalConsensusModules Man page 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
setAttr Source code
setAttrFromList 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
simpleConsensusCalculation Man page Source code
simpleHierarchicalConsensusCalculation 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
useDiskCache 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
WGCNA documentation built on March 18, 2018, 2:28 p.m.