AFcorMI Prediction of Weighted Mutual Information Adjacency Matrix by Correlation 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. WGCNA-package Weighted Gene Co-Expression Network Analysis 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 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. 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-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. 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 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 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 calculations. 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 hubGeneSignificance Hubgene significance 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 labels2colors Convert numerical labels to colors. list2multiData Convert a list to a multiData structure and vice-versa. log.na Basic Statistical Functions for Handling Missing Values 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 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.eigengeneSignificance Eigengene significance across multiple sets multiSetMEs Calculate module eigengenes. 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 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 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 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 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. 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 returnGeneSetsAsList Return pre-defined gene lists in several biomedical categories. rgcolors.func Red and Green Color Specification scaleFreeFitIndex Calculation of fitting statistics for evaluating scale free topology fit. scaleFreePlot Visual check of scale-free topology setCorrelationPreservation Summary correlation preservation measure 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 stat.bwss Between and Within Group Sum of Squares Calculation stat.diag.da Diagonal Discriminant Analysis 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