milescsmith/WGCNA
Weighted Correlation Network Analysis

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milescsmith/WGCNA: Weighted Correlation Network Analysis
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API

API for milescsmith/WGCNA
Weighted Correlation Network Analysis

Global functions
.Average Source code
.ClusterCoef.fun Source code
.MaxMean Source code
.MinMean Source code
.NPC.direct Source code
.NPC.iterate Source code
.absMaxMean Source code
.absMinMean Source code
.accuracyStatistics Man page Source code
.addErrorBars.2sided Source code
.alignedFirstPC Source code
.autoTicks Source code
.bicov Source code
.calculateIndicator Source code
.causalChildren Source code
.checkAdj Man page Source code
.checkAndDelete Source code
.checkAndScaleMultiWeights Source code
.checkAndScaleWeights Source code
.checkAvailableMemory Man page Source code
.checkComponents Source code
.checkConsistencyOfGroupAndColID Source code
.checkExpr Man page Source code
.checkListDimConsistencyAndGetDimnames Source code
.checkListNamesConsistency Source code
.checkLogicalConsistency Source code
.checkPower Source code
.choosenew Source code
.clustOrder Source code
.clusterCoeff Man page Source code Source code
.colWeightedMeans.x Source code
.colWeightedVars Source code
.collect_garbage Source code
.combineAdj Man page Source code
.computeLinksInNeighbors Man page Source code
.computeSqDiagSum Man page Source code
.consensusCalculation.base Source code
.consensusCalculation.base.FromList Source code
.consensusMEDissimilarity Source code
.corCalculation Source code
.corWeighted Source code
.corWeighted.new Source code
.coreCalcForAdj Man page Source code
.coreCalcForExpr Man page Source code
.cr.MaxMean Source code
.cr.MinMean Source code
.cr.absMaxMean Source code
.cr.absMinMean Source code
.cr.maxVariance Source code
.cvPresent Man page Source code
.devianceResidual Source code
.dimensions Source code
.dropThirdDim Source code
.effectiveNChar Source code
.emptyDist Source code
.equalizeQuantiles Source code
.err.bp Source code Source code
.euclideanDist.forNCP Source code
.extend Source code
.filterSimilarPS Source code
.getAttributesOrEmptyList Source code
.getBranchMembers Source code
.getData Source code
.getElement Source code
.getSVDs Man page Source code
.heatmap Source code
.heatmapWithLegend Source code
.hierarchicalConsensusMEDissimilarity Source code
.histogramsWithCommonBreaks Source code
.initialFit.defaultOptions Source code
.initialFit.defaultWeightName Source code
.initialFit.requiresFormula Source code
.interleave Source code
.is.adjmat Source code
.isBinary Source code
.isNumericVector Source code
.kIM Man page Source code
.linearModelCoefficients Source code
.listRep Source code
.loadAsList Source code
.loadObject Source code
.maxRowVariance Source code
.meanInRange Source code
.mergeConsensusTOMInformationLists Source code
.minTreeHeight Source code
.modulePreservationInternal Man page Source code
.mtd.checkDimConsistencyAndGetDimnames Source code
.multiPlot Source code
.nNAColors Man page Source code
.nProcessorsOnline Man page Source code
.networkCalculation Source code
.offDiagonalMatrixSum Source code
.onAttach Source code
.orderLabelsBySize Source code
.pValueFromZ Man page Source code
.panel.cor Source code
.panel.hist Source code
.permissiveDim Source code
.phyper2 Source code
.plotColorLegend Source code
.plotDendrogram Source code
.plotStandaloneLegend Source code
.processFileName Source code
.qValueFromP Man page Source code
.qorder Source code
.quickGeneVotingPredictor Source code
.quickGeneVotingPredictor.CV Source code
.restrictIndex Source code
.reverseRows Source code
.saveChunks Source code
.selectFewestMissing Source code
.setAttr Source code
.setAttrFromList Source code
.shiftList Source code
.sizeDependentQuantile Source code
.substituteTags Source code
.table2.allLevels Source code
.tableOrd Source code
.turnDistVectorIntoMatrix Source code
.turnVectorIntoDist Source code
.useDiskCache Source code
.useNThreads Man page Source code
.vector2dist Source code
.weightedScale Source code
.weightedVar Source code
AFcorMI Source code
BD.actualFileNames Source code
BD.blockLengths Source code
BD.checkAndDeleteFiles Source code
BD.getData Source code
BD.getMetaData Source code
BD.nBlocks Source code
GOenrichmentAnalysis Source code
GTOMdist Source code
TOMdist Man page Source code
TOMplot Source code
TOMsimilarity Source code
TOMsimilarityFromExpr Source code
TrueTrait Source code
WGCNAnThreads Man page Source code
accuracyMeasures Source code
addBlockToBlockwiseData Source code
addErrorBars Source code
addGrid Source code
addGuideLines Source code
addTraitToMEs Source code
adjacency Source code
adjacency.fromSimilarity Source code
adjacency.polyReg Source code
adjacency.splineReg Source code
alignExpr Source code
allocateJobs Man page Source code
allowWGCNAThreads Man page Source code
automaticNetworkScreening Source code
automaticNetworkScreeningGS Source code
bicor Source code
bicorAndPvalue Source code
bicovWeightFactors Source code
bicovWeights Source code
bicovWeightsFromFactors Source code
binarizeCategoricalColumns Source code
binarizeCategoricalColumns.forPlots Source code
binarizeCategoricalColumns.forRegression Source code
binarizeCategoricalColumns.pairwise Source code
binarizeCategoricalVariable Source code
blockSize Man page Source code
blockwiseConsensusModules Source code
blockwiseIndividualTOMs Source code
blockwiseModules Man page Source code
blueWhiteRed Source code
branchEigengeneDissim Source code
branchEigengeneSimilarity Source code
branchSplit Source code
branchSplit.dissim Source code
branchSplitFromStabilityLabels Source code
branchSplitFromStabilityLabels.individualFraction Source code
branchSplitFromStabilityLabels.prediction Source code
checkAdjMat Source code
checkSets Source code
checkSimilarity Source code
chooseOneHubInEachModule Source code
chooseTopHubInEachModule Source code
clusterCoef Source code
coClustering Source code
coClustering.permutationTest Source code
colQuantileC Source code
collapseRows Source code
collapseRowsUsingKME Source code
collectGarbage Source code
conformityBasedNetworkConcepts Source code
conformityDecomposition Source code
consensusCalculation Source code
consensusDissTOMandTree Source code
consensusKME Source code
consensusMEDissimilarity Source code
consensusOrderMEs Source code
consensusProjectiveKMeans Source code
consensusRepresentatives Source code
consensusTOM Source code
consensusTreeInputs Source code
convertNumericColumnsToNumeric Source code
cor Source code
cor1 Source code
corAndPvalue Source code
corFast Source code
corPredictionSuccess Source code
corPvalueFisher Source code
corPvalueStudent Source code
correlationPreservation Source code
coxRegressionResiduals Source code
cutreeStatic Source code
cutreeStaticColor Source code
disableWGCNAThreads Man page Source code
displayColors Source code
dynamicMergeCut Source code
empiricalBayesLM Source code
enableWGCNAThreads Man page Source code
exportNetworkToCytoscape Source code
exportNetworkToVisANT Source code
factorizeNonNumericColumns Source code
fixDataStructure Source code
formatLabels Source code
fundamentalNetworkConcepts Source code
goodGenes Source code
goodGenesMS Source code
goodSamples Source code
goodSamplesGenes Source code
goodSamplesGenesMS Source code
goodSamplesMS Source code
greenBlackRed Source code
greenWhiteRed Source code
hierarchicalBranchEigengeneDissim Source code
hierarchicalConsensusCalculation Source code
hierarchicalConsensusKME Source code
hierarchicalConsensusMEDissimilarity Source code
hierarchicalConsensusModules Source code
hierarchicalConsensusTOM Source code
hierarchicalMergeCloseModules Source code
hubGeneSignificance Source code
imputeByModule Source code
individualTOMs Source code
initProgInd Source code
intramodularConnectivity Source code
intramodularConnectivity.fromExpr Source code
isMultiData Source code
kMEcomparisonScatterplot Source code
keepCommonProbes Source code
labelPoints Source code
labeledBarplot Source code
labeledHeatmap Source code
labeledHeatmap.multiPage Source code
labels2colors Source code
list2multiData Source code
lowerTri2matrix Source code
matchLabels Source code
matrixToNetwork Source code
mergeBlockwiseData Source code
mergeCloseModules Source code
metaAnalysis Source code
metaZfunction Source code
minWhichMin Source code
moduleColor.getMEprefix Source code
moduleEigengenes Man page Source code
moduleMergeUsingKME Source code
moduleNumber Source code
modulePreservation Man page Source code
mtd.apply Source code
mtd.applyToSubset Source code
mtd.branchEigengeneDissim Source code
mtd.colnames Source code
mtd.mapply Source code
mtd.rbindSelf Source code
mtd.setAttr Source code
mtd.setColnames Source code
mtd.simplify Source code
mtd.subset Source code
multiData Source code
multiData.eigengeneSignificance Source code
multiData2list Source code
multiGSub Source code
multiGrep Source code
multiGrepl Source code
multiIntersect Source code
multiSetMEs Source code
multiSub Source code
multiUnion Source code
mutualInfoAdjacency Source code
nPresent Source code
nSets Source code
nearestCentroidPredictor Source code
nearestNeighborConnectivity Source code
nearestNeighborConnectivityMS Source code
networkConcepts Source code
networkScreening Source code
networkScreeningGS Source code
newBlockInformation Source code
newBlockwiseData Source code
newConsensusOptions Source code
newConsensusTree Source code
newCorrelationOptions Source code
newNetworkOptions Source code
normalizeLabels Source code
numbers2colors Source code
orderBranchesUsingHubGenes Source code
orderMEs Source code
orderMEsByHierarchicalConsensus Source code
overlapTable Source code
overlapTableUsingKME Source code
pickHardThreshold Source code
pickHardThreshold.fromSimilarity Source code
pickSoftThreshold Man page Source code
pickSoftThreshold.fromSimilarity Source code
plotClusterTreeSamples Source code
plotColorUnderTree Source code
plotCor Source code
plotDendroAndColors Source code
plotEigengeneNetworks Source code
plotMEpairs Source code
plotMat Source code
plotModuleSignificance Source code
plotMultiHist Source code
plotNetworkHeatmap Source code
plotOrderedColors Source code
pmean Source code
pmean.fromList Source code
pmedian Source code
pminWhich.fromList Source code
populationMeansInAdmixture Source code
pquantile Source code
pquantile.fromList Source code
prepComma Source code
prependZeros Source code
preservationNetworkConnectivity Source code
projectiveKMeans Source code
propVarExplained Source code
pruneAndMergeConsensusModules Source code
pruneConsensusModules Source code
qvalue Source code
qvalue.restricted Source code
randIndex Source code
rankPvalue Source code
recutBlockwiseTrees Source code
recutConsensusTrees Source code
redWhiteGreen Source code
reflectBranch Source code
relativeCorPredictionSuccess Source code
removeGreyME Source code
removePrincipalComponents Source code
replaceMissing Source code
returnGeneSetsAsList Source code
rgcolors.func Source code
rowQuantileC Source code
sampledBlockwiseModules Source code
sampledHierarchicalConsensusModules Source code
scaleFreeFitIndex Source code
scaleFreePlot Source code
selectBranch Source code
selectFewestConsensusMissing Source code
setCorrelationPreservation Source code
shortenStrings Source code
sigmoidAdjacencyFunction Source code
signedKME Source code
signifNumeric Source code
signumAdjacencyFunction Source code
simpleConsensusCalculation Source code
simpleHierarchicalConsensusCalculation Source code
simulateDatExpr Source code
simulateDatExpr5Modules Source code
simulateEigengeneNetwork Source code
simulateModule Source code
simulateMultiExpr Source code
simulateSmallLayer Source code
sizeGrWindow Source code
softConnectivity Source code
softConnectivity.fromSimilarity Source code
spaste Source code
standardColors Source code
standardScreeningBinaryTrait Source code
standardScreeningCensoredTime Source code
standardScreeningNumericTrait Source code
stdErr Source code
stratifiedBarplot Source code
subsetTOM Source code
swapTwoBranches Source code
transposeBigData Source code
unsignedAdjacency Source code
updateProgInd Source code
userListEnrichment Source code
vectorTOM Source code
vectorizeMatrix Source code
verboseBarplot Source code
verboseBoxplot Source code
verboseIplot Source code
verboseScatterplot Source code
votingLinearPredictor Source code
milescsmith/WGCNA documentation built on April 11, 2024, 1:26 a.m.

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