AFcorMI                 Prediction of Weighted Mutual Information
                        Adjacency Matrix by Correlation
BD.getData              Various basic operations on 'BlockwiseData'
                        objects.
BloodLists              Blood Cell Types with Corresponding Gene
                        Markers
BrainLists              Brain-Related Categories with Corresponding
                        Gene Markers
BrainRegionMarkers      Gene Markers for Regions of the Human Brain
GOenrichmentAnalysis    Calculation of GO enrichment (experimental)
GTOMdist                Generalized Topological Overlap Measure
ImmunePathwayLists      Immune Pathways with Corresponding Gene Markers
PWLists                 Pathways with Corresponding Gene Markers -
                        Compiled by Mike Palazzolo and Jim Wang from
                        CHDI
SCsLists                Stem Cell-Related Genes with Corresponding Gene
                        Markers
TOMplot                 Graphical representation of the Topological
                        Overlap Matrix
TOMsimilarity           Topological overlap matrix similarity and
                        dissimilarity
TOMsimilarityFromExpr   Topological overlap matrix
TrueTrait               Estimate the true trait underlying a list of
                        surrogate markers.
accuracyMeasures        Accuracy measures for a 2x2 confusion matrix or
                        for vectors of predicted and observed values.
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 regression
alignExpr               Align expression data with given vector
allocateJobs            Divide tasks among workers
allowWGCNAThreads       Allow and disable multi-threading for certain
                        WGCNA calculations
automaticNetworkScreening
                        One-step automatic network gene screening
automaticNetworkScreeningGS
                        One-step automatic network gene screening with
                        external gene significance
bicor                   Biweight Midcorrelation
bicorAndPvalue          Calculation of biweight midcorrelations and
                        associated p-values
bicovWeights            Weights used in biweight midcovariance
binarizeCategoricalColumns
                        Turn categorical columns into sets of binary
                        indicators
binarizeCategoricalVariable
                        Turn a categorical variable into a set of
                        binary indicators
blockSize               Attempt to calculate an appropriate block size
                        to maximize efficiency of block-wise
                        calcualtions.
blockwiseConsensusModules
                        Find consensus modules across several datasets.
blockwiseIndividualTOMs
                        Calculation of block-wise topological overlaps
blockwiseModules        Automatic network construction and module
                        detection
blueWhiteRed            Blue-white-red color sequence
branchEigengeneDissim   Branch dissimilarity based on eigennodes
                        (eigengenes).
branchSplit             Branch split.
branchSplit.dissim      Branch split based on dissimilarity.
branchSplitFromStabilityLabels
                        Branch split (dissimilarity) statistics derived
                        from labels determined from a stability study
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 clusterings
coClustering.permutationTest
                        Permutation test for co-clustering
colQuantileC            Fast colunm- and row-wise quantile of a matrix.
collapseRows            Select one representative row per group
collapseRowsUsingKME    Selects one representative row per group based
                        on kME
collectGarbage          Iterative garbage collection.
conformityBasedNetworkConcepts
                        Calculation of conformity-based network
                        concepts.
conformityDecomposition
                        Conformity and module based decomposition of a
                        network adjacency matrix.
consensusCalculation    Calculation of a (single) consenus with
                        optional data calibration.
consensusDissTOMandTree
                        Consensus clustering based on topological
                        overlap and hierarchical clustering
consensusKME            Calculate consensus kME (eigengene-based
                        connectivities) across multiple data sets.
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 data
consensusRepresentatives
                        Consensus selection of group representatives
consensusTOM            Consensus network (topological overlap).
consensusTreeInputs     Get all elementary inputs in a consensus tree
convertNumericColumnsToNumeric
                        Convert character columns that represent
                        numbers to numeric
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 model
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
factorizeNonNumericColumns
                        Turn non-numeric columns into factors
fixDataStructure        Put single-set data into a form useful for
                        multiset calculations.
formatLabels            Break long character strings into multiple
                        lines
fundamentalNetworkConcepts
                        Calculation of fundamental network concepts
                        from an adjacency matrix.
goodGenes               Filter genes with too many missing entries
goodGenesMS             Filter genes with too many missing entries
                        across multiple sets
goodSamples             Filter samples with too many missing entries
goodSamplesGenes        Iterative filtering of samples and genes with
                        too many missing entries
goodSamplesGenesMS      Iterative filtering of samples and genes with
                        too many missing entries across multiple data
                        sets
goodSamplesMS           Filter samples with too many missing entries
                        across multiple data sets
greenBlackRed           Green-black-red color sequence
greenWhiteRed           Green-white-red color sequence
hierarchicalConsensusCalculation
                        Hierarchical consensus calculation
hierarchicalConsensusKME
                        Calculation of measures of fuzzy module
                        membership (KME) in hierarchical consensus
                        modules
hierarchicalConsensusMEDissimilarity
                        Hierarchical consensus calculation of module
                        eigengene dissimilarity
hierarchicalConsensusModules
                        Hierarchical consensus network construction and
                        module identification
hierarchicalConsensusTOM
                        Calculation of hierarchical consensus
                        topological overlap matrix
hierarchicalMergeCloseModules
                        Merge close (similar) hierarchical consensus
                        modules
hubGeneSignificance     Hubgene significance
imputeByModule          Impute missing data separately in each module
individualTOMs          Calculate individual correlation network
                        matrices
initProgInd             Inline display of progress
intramodularConnectivity
                        Calculation of intramodular connectivity
isMultiData             Determine whether the supplied object is a
                        valid multiData structure
kMEcomparisonScatterplot
                        Function to plot kME values between two
                        comparable data sets.
keepCommonProbes        Keep probes that are shared among given data
                        sets
labelPoints             Label scatterplot points
labeledBarplot          Barplot with text or color labels.
labeledHeatmap          Produce a labeled heatmap plot
labeledHeatmap.multiPage
                        Labeled heatmap divided into several separate
                        plots.
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
                        (lower-triangular) representation
matchLabels             Relabel module labels to best match the given
                        reference labels
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
minWhichMin             Fast joint calculation of row- or column-wise
                        minima and indices of minimum elements
modifiedBisquareWeights
                        Modified Bisquare Weights
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 frame.
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 3-dimensional array.
mtd.subset              Subset rows and columns in a multiData
                        structure
multiData               Create a multiData structure.
multiData.eigengeneSignificance
                        Eigengene significance across multiple sets
multiGSub               Analogs of grep(l) and (g)sub for multiple
                        patterns and relacements
multiSetMEs             Calculate module eigengenes.
multiUnion              Union and intersection of multiple sets
mutualInfoAdjacency     Calculate weighted adjacency matrices based on
                        mutual information
nPresent                Number of present data entries.
nSets                   Number of sets in a multi-set variable
nearestCentroidPredictor
                        Nearest centroid predictor
nearestNeighborConnectivity
                        Connectivity to a constant number of nearest
                        neighbors
nearestNeighborConnectivityMS
                        Connectivity to a constant number of nearest
                        neighbors across multiple data sets
networkConcepts         Calculations of network concepts
networkScreening        Identification of genes related to a trait
networkScreeningGS      Network gene screening with an external gene
                        significance measure
newBlockInformation     Create a list holding information about
                        dividing data into blocks
newBlockwiseData        Create, merge and expand BlockwiseData objects
newConsensusOptions     Create a list holding consensus calculation
                        options.
newConsensusTree        Create a new consensus tree
newCorrelationOptions   Creates a list of correlation options.
newNetworkOptions       Create a list of network construction arguments
                        (options).
normalizeLabels         Transform numerical labels into normal order.
numbers2colors          Color representation for a numeric variable
orderBranchesUsingHubGenes
                        Optimize dendrogram using branch swaps and
                        reflections.
orderMEs                Put close eigenvectors next to each other
orderMEsByHierarchicalConsensus
                        Order module eigengenes by their hierarchical
                        consensus similarity
overlapTable            Calculate overlap of modules
overlapTableUsingKME    Determines significant overlap between modules
                        in two networks based on kME tables.
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 dendrogram
plotCor                 Red and Green Color Image of Correlation Matrix
plotDendroAndColors     Dendrogram plot with color annotation of
                        objects
plotEigengeneNetworks   Eigengene network plot
plotMEpairs             Pairwise scatterplots of eigengenes
plotMat                 Red and Green Color Image of Data Matrix
plotModuleSignificance
                        Barplot of module significance
plotMultiHist           Plot multiple histograms in a single plot
plotNetworkHeatmap      Network heatmap plot
populationMeansInAdmixture
                        Estimate the population-specific mean values in
                        an admixed population.
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
propVarExplained        Proportion of variance explained by eigengenes.
proportionsInAdmixture
                        Estimate the proportion of pure populations in
                        an admixed population based on marker
                        expression values.
pruneAndMergeConsensusModules
                        Iterative pruning and merging of (hierarchical)
                        consensus modules
pruneConsensusModules   Prune (hierarchical) consensus modules by
                        removing genes with low eigengene-based
                        intramodular connectivity
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) on multiple lists
recutBlockwiseTrees     Repeat blockwise module detection from
                        pre-calculated data
recutConsensusTrees     Repeat blockwise consensus module detection
                        from pre-calculated data
redWhiteGreen           Red-white-green color sequence
relativeCorPredictionSuccess
                        Compare prediction success
removeGreyME            Removes the grey eigengene from a given
                        collection of eigengenes.
removePrincipalComponents
                        Remove leading principal components from data
replaceMissing          Replace missing values with a constant.
returnGeneSetsAsList    Return pre-defined gene lists in several
                        biomedical categories.
rgcolors.func           Red and Green Color Specification
sampledBlockwiseModules
                        Blockwise module identification in sampled data
sampledHierarchicalConsensusModules
                        Hierarchical consensus module identification in
                        sampled data
scaleFreeFitIndex       Calculation of fitting statistics for
                        evaluating scale free topology fit.
scaleFreePlot           Visual check of scale-free topology
selectFewestConsensusMissing
                        Select columns with the lowest consensus number
                        of missing data
setCorrelationPreservation
                        Summary correlation preservation measure
shortenStrings          Shorten given character strings by truncating
                        at a suitable separator.
sigmoidAdjacencyFunction
                        Sigmoid-type adacency function.
signedKME               Signed eigengene-based connectivity
signifNumeric           Round numeric columns to given significant
                        digits.
signumAdjacencyFunction
                        Hard-thresholding adjacency function
simpleConsensusCalculation
                        Simple calculation of a single consenus
simpleHierarchicalConsensusCalculation
                        Simple hierarchical consensus calculation
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
sizeRestrictedClusterMerge
                        Cluter merging with size restrictions
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.
transposeBigData        Transpose a big matrix or data frame
unsignedAdjacency       Calculation of unsigned adjacency
userListEnrichment      Measure enrichment between inputted and
                        user-defined lists
vectorTOM               Topological overlap for a subset of the whole
                        set of genes
vectorizeMatrix         Turn a matrix into a vector of non-redundant
                        components
verboseBarplot          Barplot with error bars, annotated by
                        Kruskal-Wallis or ANOVA p-value
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
