![[R logo]](../../../doc/html/logo.jpg){kind=logo}
![[Up]](../../../doc/html/left.jpg){kind=small}
![[Top]](../../../doc/html/up.jpg){kind=small}
A B C D E F G H I K L M N O P Q R S T U V W
| WGCNA-package | Weighted Gene Co-Expression Network Analysis |
| 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.fromSimilarity | Calculate network adjacency |
| alignExpr | Align expression data with given vector |
| automaticNetworkScreening | One-step automatic network gene screening |
| automaticNetworkScreeningGS | One-step automatic network gene screening with external gene significance |
| AUV2predicted | Prediction of Weighted Mutual Information Adjacency Matrix by Correlation |
| bicor | Biweight Midcorrelation |
| bicorAndPvalue | Calculation of biweight midcorrelations and associated p-values |
| blockwiseConsensusModules | Find consensus modules across several datasets. |
| blockwiseModules | Automatic network construction and module detection |
| checkAdjMat | Check adjacency matrix |
| checkSets | Check structure and retrieve sizes of a group of datasets. |
| checkSimilarity | Check adjacency matrix |
| clusterCoef | Clustering coefficient calculation |
| collapseRows | Select one representative row per group |
| collectGarbage | Iterative garbage collection. |
| colQuantileC | Fast colunm-wise quantile of a matrix. |
| conformityBasedNetworkConcepts | Calculation of conformity-based network concepts. |
| 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. |
| cor.na | Basic Statistical Functions for Handling Missing Values |
| cor1 | Fast calculations of Pearson correlation. |
| corAndPvalue | Calculation of correlations and associated p-values |
| corFast | Fast calculations of Pearson correlation. |
| 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 |
| 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. |
| GOenrichmentAnalysis | Calculation of GO enrichment (experimental) |
| 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 |
| GTOMdist | Generalized Topological Overlap Measure |
| hubGeneSignificance | Hubgene significance |
| initProgInd | Inline display of progress |
| intramodularConnectivity | Calculation of intramodular connectivity |
| keepCommonProbes | Keep probes that are shared among given data sets |
| labeledBarplot | Barplot with text or color labels. |
| labeledHeatmap | Produce a labeled heatmap plot |
| labelPoints | Label scatterplot points |
| labels2colors | Convert numerical labels to colors. |
| length.na | Basic Statistical Functions for Handling Missing Values |
| log.na | Basic Statistical Functions for Handling Missing Values |
| matchLabels | Relabel module labels to best match the given reference labels |
| mean.na | Basic Statistical Functions for Handling Missing Values |
| mergeCloseModules | Merge close modules in gene expression data |
| metaZfunction | Meta-analysis Z statistic |
| moduleColor.getMEprefix | Get the prefix used to label module eigengenes. |
| moduleEigengenes | Calculate module eigengenes. |
| moduleNumber | Fixed-height cut of a dendrogram. |
| modulePreservation | Calculation of module preservation statistics |
| multiSetMEs | Calculate module eigengenes. |
| mutualInfoAdjacency | Calculate weighted adjacency matrices based on mutual information |
| 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. |
| nPresent | Number of present data entries. |
| numbers2colors | Color representation for a numeric variable |
| order.na | Basic Statistical Functions for Handling Missing Values |
| orderMEs | Put close eigenvectors next to each other |
| overlapTable | Calculate overlap of modules |
| pickHardThreshold | Analysis of scale free topology for hard-thresholding. |
| pickHardThreshold.fromSimilarity | Analysis of scale free topology for hard-thresholding. |
| pickSoftThreshold | Analysis of scale free topology for soft-thresholding |
| pickSoftThreshold.fromSimilarity | Analysis of scale free topology for soft-thresholding |
| plot.cor | Red and Green Color Image of Correlation Matrix |
| plot.mat | Red and Green Color Image of Data Matrix |
| plotClusterTreeSamples | Annotated clustering dendrogram of microarray samples |
| plotColorUnderTree | Plot color rows under a dendrogram |
| plotDendroAndColors | Dendrogram plot with color annotation of objects |
| plotEigengeneNetworks | Eigengene network plot |
| plotMEpairs | Pairwise scatterplots of eigengenes |
| plotModuleSignificance | Barplot of module significance |
| plotNetworkHeatmap | Network heatmap plot |
| pmean | Parallel quantile, median, mean |
| pmedian | Parallel quantile, median, mean |
| pquantile | Parallel quantile, median, mean |
| prepComma | Prepend a comma to a non-empty string |
| preservationNetworkConnectivity | Network preservation calculations |
| prod.na | Basic Statistical Functions for Handling Missing Values |
| projectiveKMeans | Projective K-means (pre-)clustering of expression data |
| propVarExplained | Proportion of variance explained by eigengenes. |
| quantile.na | Basic Statistical Functions for Handling Missing Values |
| 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. |
| rgcolors.func | Red and Green Color Specification |
| scale.na | Basic Statistical Functions for Handling Missing Values |
| 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. |
| softConnectivity.fromSimilarity | 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. |
| subsetTOM | Topological overlap for a subset of a whole set of genes |
| sum.na | Basic Statistical Functions for Handling Missing Values |
| TOMdist | Topological overlap matrix similarity and dissimilarity |
| TOMplot | Graphical representation of the Topological Overlap Matrix |
| TOMsimilarity | Topological overlap matrix similarity and dissimilarity |
| TOMsimilarityFromExpr | Topological overlap matrix |
| unsignedAdjacency | Calculation of unsigned adjacency |
| updateProgInd | Inline display of progress |
| var.na | Basic Statistical Functions for Handling Missing Values |
| 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 p-value |
| verboseBoxplot | Boxplot annotated by a Kruskal-Wallis p-value |
| verboseScatterplot | Scatterplot annotated by regression line and p-value |
| WGCNA | Weighted Gene Co-Expression Network Analysis |