Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
|Author||Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang|
|Date of publication||2016-03-15 00:24:08|
|Maintainer||Peter Langfelder <Peter.Langfelder@gmail.com>|
|License||GPL (>= 2)|
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...
bicor: Biweight Midcorrelation
bicorAndPvalue: Calculation of biweight midcorrelations and associated...
bicovWeights: Weights used in biweight midcovariance
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) statistic 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...
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).
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
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
hubGeneSignificance: Hubgene significance
ImmunePathwayLists: Immune Pathways with Corresponding Gene Markers
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
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
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...
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
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
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.
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
returnGeneSetsAsList: Return pre-defined gene lists in several biomedical...
rgcolors.func: Red and Green Color Specification
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
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
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
WGCNA-package: Weighted Gene Co-Expression Network Analysis