Weighted Correlation Network Analysis

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... |

BD.getData | Various basic operations on 'BlockwiseData' objects. |

bicor | Biweight Midcorrelation |

bicorAndPvalue | Calculation of biweight midcorrelations and associated... |

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... |

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) statistics 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... |

consensusCalculation | Calculation of a (single) consenus with optional data... |

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). |

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... |

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... |

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 |

hierarchicalConsensusCalculation | Hierarchical consensus calculation |

hierarchicalConsensusKME | Calculation of measures of fuzzy module membership (KME) in... |

hierarchicalConsensusMEDissimilarity | Hierarchical consensus calculation of module eigengene... |

hierarchicalConsensusModules | Hierarchical consensus network construction and module... |

hierarchicalConsensusTOM | Calculation of hierarchical consensus topological overlap... |

hierarchicalMergeCloseModules | Merge close (similar) hierarchical consensus modules |

hubGeneSignificance | Hubgene significance |

ImmunePathwayLists | Immune Pathways with Corresponding Gene Markers |

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... |

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 |

minWhichMin | Fast joint calculation of row- or column-wise minima and... |

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 |

multiGSub | Analogs of grep(l) and (g)sub for multiple patterns and... |

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... |

newBlockInformation | Create a list holding information about dividing data into... |

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. |

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 |

orderMEsByHierarchicalConsensus | Order module eigengenes by their hierarchical consensus... |

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 |

plotMultiHist | Plot multiple histograms in a single plot |

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. |

pruneAndMergeConsensusModules | Iterative pruning and merging of (hierarchical) consensus... |

pruneConsensusModules | Prune (hierarchical) consensus modules by removing genes with... |

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 |

replaceMissing | Replace missing values with a constant. |

returnGeneSetsAsList | Return pre-defined gene lists in several biomedical... |

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... |

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 |

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. |

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 |

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