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Install
install.packages('WGCNA')
Monthly Downloads
24,286
Version
1.68
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
May 23rd, 2019
Functions in WGCNA (1.68)
Search functions
GTOMdist
Generalized Topological Overlap Measure
TOMsimilarityFromExpr
Topological overlap matrix
alignExpr
Align expression data with given vector
allocateJobs
Divide tasks among workers
TrueTrait
Estimate the true trait underlying a list of surrogate markers.
blockwiseIndividualTOMs
Calculation of block-wise topological overlaps
blockwiseModules
Automatic network construction and module detection
branchSplitFromStabilityLabels
Branch split (dissimilarity) statistics derived from labels determined from a stability study
checkAdjMat
Check adjacency matrix
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
consensusTreeInputs
Get all elementary inputs in a consensus tree
convertNumericColumnsToNumeric
Convert character columns that represent numbers to numeric
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.
PWLists
Pathways with Corresponding Gene Markers - Compiled by Mike Palazzolo and Jim Wang from CHDI
hierarchicalConsensusCalculation
Hierarchical consensus calculation
SCsLists
Stem Cell-Related Genes with Corresponding Gene Markers
hierarchicalConsensusKME
Calculation of measures of fuzzy module membership (KME) in hierarchical consensus modules
labelPoints
Label scatterplot points
TOMplot
Graphical representation of the Topological Overlap Matrix
labeledBarplot
Barplot with text or color labels.
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
metaAnalysis
Meta-analysis of binary and continuous variables
metaZfunction
Meta-analysis Z statistic
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
mtd.rbindSelf
Turn a multiData structure into a single matrix or data frame.
chooseTopHubInEachModule
Chooses the top hub gene in each module
clusterCoef
Clustering coefficient calculation
collapseRowsUsingKME
Selects one representative row per group based on kME
collectGarbage
Iterative garbage collection.
mtd.setAttr
Set attributes on each component of a multiData structure
multiSetMEs
Calculate module eigengenes.
consensusRepresentatives
Consensus selection of group representatives
consensusTOM
Consensus network (topological overlap).
multiUnion
Union and intersection of multiple sets
exportNetworkToCytoscape
Export network to Cytoscape
BrainRegionMarkers
Gene Markers for Regions of the Human Brain
exportNetworkToVisANT
Export network data in format readable by VisANT
newNetworkOptions
Create a list of network construction arguments (options).
greenBlackRed
Green-black-red color sequence
greenWhiteRed
Green-white-red color sequence
normalizeLabels
Transform numerical labels into normal order.
BloodLists
Blood Cell Types with Corresponding Gene Markers
hubGeneSignificance
Hubgene significance
imputeByModule
Impute missing data separately in each module
labels2colors
Convert numerical labels to colors.
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix or for vectors of predicted and observed values.
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
BrainLists
Brain-Related Categories with Corresponding Gene Markers
addErrorBars
Add error bars to a barplot.
allowWGCNAThreads
Allow and disable multi-threading for certain WGCNA calculations
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
plotMat
Red and Green Color Image of Data Matrix
projectiveKMeans
Projective K-means (pre-)clustering of expression data
plotModuleSignificance
Barplot of module significance
list2multiData
Convert a list to a multiData structure and vice-versa.
preservationNetworkConnectivity
Network preservation calculations
minWhichMin
Fast joint calculation of row- or column-wise minima and indices of minimum elements
addTraitToMEs
Add trait information to multi-set module eigengene structure
adjacency
Calculate network adjacency
adjacency.polyReg
Adjacency matrix based on polynomial regression
automaticNetworkScreening
One-step automatic network gene screening
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
moduleNumber
Fixed-height cut of a dendrogram.
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
modulePreservation
Calculation of module preservation statistics
branchSplit
Branch split.
branchSplit.dissim
Branch split based on dissimilarity.
checkSets
Check structure and retrieve sizes of a group of datasets.
chooseOneHubInEachModule
Chooses a single hub gene in each module
redWhiteGreen
Red-white-green color sequence
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
blockSize
Attempt to calculate an appropriate block size to maximize efficiency of block-wise calcualtions.
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
corPvalueStudent
Student asymptotic p-value for correlation
BD.getData
Various basic operations on
BlockwiseData
objects.
correlationPreservation
Preservation of eigengene correlations
addGrid
Add grid lines to an existing plot.
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
cutreeStatic
Constant-height tree cut
blockwiseConsensusModules
Find consensus modules across several datasets.
relativeCorPredictionSuccess
Compare prediction success
goodSamples
Filter samples with too many missing entries
coClustering
Co-clustering measure of cluster preservation between two clusterings
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
individualTOMs
Calculate individual correlation network matrices
nSets
Number of sets in a multi-set variable
nearestCentroidPredictor
Nearest centroid predictor
newConsensusTree
Create a new consensus tree
newCorrelationOptions
Creates a list of correlation options.
bicor
Biweight Midcorrelation
scaleFreePlot
Visual check of scale-free topology
blueWhiteRed
Blue-white-red color sequence
selectFewestConsensusMissing
Select columns with the lowest consensus number of missing data
coClustering.permutationTest
Permutation test for co-clustering
numbers2colors
Color representation for a numeric variable
colQuantileC
Fast colunm- and row-wise quantile of a matrix.
Inline display of progress
Inline display of progress
branchEigengeneDissim
Branch dissimilarity based on eigennodes (eigengenes).
collapseRows
Select one representative row per group
intramodularConnectivity
Calculation of intramodular connectivity
consensusKME
Calculate consensus kME (eigengene-based connectivities) across multiple data sets.
consensusCalculation
Calculation of a (single) consenus with optional data calibration.
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
corPredictionSuccess
Qunatification of success of gene screening
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
plotEigengeneNetworks
Eigengene network plot
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
isMultiData
Determine whether the supplied object is a valid multiData structure
corPvalueFisher
Fisher's asymptotic p-value for correlation
lowerTri2matrix
Reconstruct a symmetric matrix from a distance (lower-triangular) representation
cor
Fast calculations of Pearson correlation.
plotMEpairs
Pairwise scatterplots of eigengenes
matchLabels
Relabel module labels to best match the given reference labels
propVarExplained
Proportion of variance explained by eigengenes.
corAndPvalue
Calculation of correlations and associated p-values
dynamicMergeCut
Threshold for module merging
mtd.apply
Apply a function to each set in a multiData structure.
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
mtd.mapply
Apply a function to elements of given multiData structures.
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
cutreeStaticColor
Constant height tree cut using color labels
displayColors
Show colors used to label modules
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
goodGenes
Filter genes with too many missing entries
empiricalBayesLM
Empirical Bayes-moderated adjustment for unwanted covariates
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
goodGenesMS
Filter genes with too many missing entries across multiple sets
simulateEigengeneNetwork
Simulate eigengene network from a causal model
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
hierarchicalConsensusTOM
Calculation of hierarchical consensus topological overlap matrix
networkScreeningGS
Network gene screening with an external gene significance measure
simulateModule
Simulate a gene co-expression module
newBlockInformation
Create a list holding information about dividing data into blocks
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
hierarchicalMergeCloseModules
Merge close (similar) hierarchical consensus modules
labeledHeatmap
Produce a labeled heatmap plot
hierarchicalConsensusMEDissimilarity
Hierarchical consensus calculation of module eigengene dissimilarity
overlapTable
Calculate overlap of modules
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
hierarchicalConsensusModules
Hierarchical consensus network construction and module identification
keepCommonProbes
Keep probes that are shared among given data sets
stdErr
Standard error of the mean of a given vector.
labeledHeatmap.multiPage
Labeled heatmap divided into several separate plots.
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
moduleEigengenes
Calculate module eigengenes.
signedKME
Signed eigengene-based connectivity
matrixToNetwork
Construct a network from a matrix
moduleMergeUsingKME
Merge modules and reassign genes using kME.
stratifiedBarplot
Bar plots of data across two splitting parameters
userListEnrichment
Measure enrichment between inputted and user-defined lists
mergeCloseModules
Merge close modules in gene expression data
mtd.setColnames
Get and set column names in a multiData structure.
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
vectorTOM
Topological overlap for a subset of the whole set of genes
mtd.simplify
If possible, simplify a multiData structure to a 3-dimensional array.
pquantile
Parallel quantile, median, mean
multiData.eigengeneSignificance
Eigengene significance across multiple sets
simulateDatExpr
Simulation of expression data
mtd.subset
Subset rows and columns in a multiData structure
multiData
Create a multiData structure.
multiGSub
Analogs of grep(l) and (g)sub for multiple patterns and relacements
networkConcepts
Calculations of network concepts
simulateDatExpr5Modules
Simplified simulation of expression data
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
nPresent
Number of present data entries.
newBlockwiseData
Create, merge and expand BlockwiseData objects
sizeGrWindow
Opens a graphics window with specified dimensions
newConsensusOptions
Create a list holding consensus calculation options.
orderMEs
Put close eigenvectors next to each other
qvalue
Estimate the q-values for a given set of p-values
orderMEsByHierarchicalConsensus
Order module eigengenes by their hierarchical consensus similarity
qvalue.restricted
qvalue convenience wrapper
networkScreening
Identification of genes related to a trait
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
plotMultiHist
Plot multiple histograms in a single plot
replaceMissing
Replace missing values with a constant.
returnGeneSetsAsList
Return pre-defined gene lists in several biomedical categories.
plotNetworkHeatmap
Network heatmap plot
pruneAndMergeConsensusModules
Iterative pruning and merging of (hierarchical) consensus modules
sizeRestrictedClusterMerge
Cluter merging with size restrictions
pruneConsensusModules
Prune (hierarchical) consensus modules by removing genes with low eigengene-based intramodular connectivity
transposeBigData
Transpose a big matrix or data frame
unsignedAdjacency
Calculation of unsigned adjacency
prepComma
Prepend a comma to a non-empty string
rgcolors.func
Red and Green Color Specification
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
removePrincipalComponents
Remove leading principal components from data
sampledBlockwiseModules
Blockwise module identification in sampled data
sampledHierarchicalConsensusModules
Hierarchical consensus module identification in sampled data
prependZeros
Pad numbers with leading zeros to specified total width
simpleConsensusCalculation
Simple calculation of a single consenus
simpleHierarchicalConsensusCalculation
Simple hierarchical consensus calculation
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
softConnectivity
Calculates connectivity of a weighted network.
simulateMultiExpr
Simulate multi-set expression data
simulateSmallLayer
Simulate small modules
spaste
Space-less paste
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
standardColors
Colors this library uses for labeling modules.
randIndex
Rand index of two partitions
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
verboseIplot
Scatterplot with density
standardScreeningBinaryTrait
Standard screening for binatry traits
subsetTOM
Topological overlap for a subset of a whole set of genes
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
verboseScatterplot
Scatterplot annotated by regression line and p-value
setCorrelationPreservation
Summary correlation preservation measure
votingLinearPredictor
Voting linear predictor
shortenStrings
Shorten given character strings by truncating at a suitable separator.
signifNumeric
Round numeric columns to given significant digits.
signumAdjacencyFunction
Hard-thresholding adjacency function
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
standardScreeningNumericTrait
Standard screening for numeric traits
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
ImmunePathwayLists
Immune Pathways with Corresponding Gene Markers