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WGCNA (version 1.20)
Weighted Correlation Network Analysis
Description
Functions necessary to perform Weighted Correlation Network Analysis
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Install
install.packages('WGCNA')
Monthly Downloads
18,389
Version
1.20
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
April 24th, 2012
Functions in WGCNA (1.20)
Search functions
consensusKME
Calculate consensus kME (eigengene-based connectivities) across multiple data sets.
TOMsimilarityFromExpr
Topological overlap matrix
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
blockwiseModules
Automatic network construction and module detection
displayColors
Show colors used to label modules
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
collectGarbage
Iterative garbage collection.
collapseRows
Select one representative row per group
clusterCoef
Clustering coefficient calculation
moduleMergeUsingKME
Merge modules and reassign genes using kME.
GTOMdist
Generalized Topological Overlap Measure
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
labelPoints
Label scatterplot points
chooseOneHubInEachModule
Chooses a single hub gene in each module
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
SCsLists
Stem Cell-Related Genes with Corresponding Gene Markers
Inline display of progress
Inline display of progress
adjacency.polyReg
Adjacency matrix based on polynomial regression
networkConcepts
Calculations of network concepts
exportNetworkToVisANT
Export network data in format readable by VisANT
coClustering.permutationTest
Permutation test for co-clustering
colQuantileC
Fast colunm-wise quantile of a matrix.
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
nSets
Number of sets in a multi-set variable
exportNetworkToCytoscape
Export network to Cytoscape
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
BloodLists
Blood Cell Types with Corresponding Gene Markers
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
matrixToNetwork
Construct a network from a matrix
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
addTraitToMEs
Add trait information to multi-set module eigengene structure
metaZfunction
Meta-analysis Z statistic
TrueTrait
Estimate the true trait underlying a list of surrogate markers.
checkAdjMat
Check adjacency matrix
hubGeneSignificance
Hubgene significance
collapseRowsUsingKME
Selects one representative row per group based on kME
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
coClustering
Co-clustering measure of cluster preservation between two clusterings
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
corPvalueFisher
Fisher's asymptotic p-value for correlation
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
greenBlackRed
Green-black-red color sequence
checkSets
Check structure and retrieve sizes of a group of datasets.
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
metaAnalysis
Meta-analysis of binary and continuous variables
blockwiseIndividualTOMs
Calculation of block-wise topological overlaps
modulePreservation
Calculation of module preservation statistics
labeledBarplot
Barplot with text or color labels.
intramodularConnectivity
Calculation of intramodular connectivity
BrainLists
Brain-Related Categories with Corresponding Gene Markers
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
blockwiseConsensusModules
Find consensus modules across several datasets.
chooseTopHubInEachModule
Chooses the top hub gene in each module
plotDendroAndColors
Dendrogram plot with color annotation of objects
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
stat.bwss
Between and Within Group Sum of Squares Calculation
standardScreeningBinaryTrait
Standard screening for binatry traits
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
keepCommonProbes
Keep probes that are shared among given data sets
prepComma
Prepend a comma to a non-empty string
cutreeStatic
Constant-height tree cut
nPresent
Number of present data entries.
correlationPreservation
Preservation of eigengene correlations
normalizeLabels
Transform numerical labels into normal order.
TOMplot
Graphical representation of the Topological Overlap Matrix
simulateDatExpr5Modules
Simplified simulation of expression data
mergeCloseModules
Merge close modules in gene expression data
stratifiedBarplot
Bar plots of data across two splitting parameters
pquantile
Parallel quantile, median, mean
qvalue
Estimate the q-values for a given set of p-values
bicor
Biweight Midcorrelation
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
automaticNetworkScreening
One-step automatic network gene screening
softConnectivity
Calculates connectivity of a weighted network.
signumAdjacencyFunction
Hard-thresholding adjacency function
labeledHeatmap
Produce a labeled heatmap plot
corPvalueStudent
Student asymptotic p-value for correlation
multiData.eigengeneSignificance
Eigengene significance across multiple sets
blueWhiteRed
Blue-white-red color sequence
numbers2colors
Color representation for a numeric variable
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix.
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
votingLinearPredictor
Voting linear predictor
plotEigengeneNetworks
Eigengene network plot
dynamicMergeCut
Threshold for module merging
userListEnrichment
Measure enrichment between inputted and user-defined lists
allowWGCNAThreads
Allow and disable multi-threading for certain WGCNA calculations
na
Basic Statistical Functions for Handling Missing Values
cutreeStaticColor
Constant height tree cut using color labels
plotColorUnderTree
Plot color rows under a dendrogram
WGCNA-package
Weighted Gene Co-Expression Network Analysis
labels2colors
Convert numerical labels to colors.
goodGenes
Filter genes with too many missing entries
simulateDatExpr
Simulation of expression data
stat.diag.da
Diagonal Discriminant Analysis
projectiveKMeans
Projective K-means (pre-)clustering of expression data
cor
Fast calculations of Pearson correlation.
corPredictionSuccess
Qunatification of success of gene screening
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
adjacency
Calculate network adjacency
multiSetMEs
Calculate module eigengenes.
fixDataStructure
Put single-set data into a form useful for multiset calculations.
alignExpr
Align expression data with given vector
networkScreeningGS
Network gene screening with an external gene significance measure
overlapTable
Calculate overlap of modules
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
plotModuleSignificance
Barplot of module significance
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
networkScreening
Identification of genes related to a trait
moduleNumber
Fixed-height cut of a dendrogram.
orderMEs
Put close eigenvectors next to each other
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
standardColors
Colors this library uses for labeling modules.
relativeCorPredictionSuccess
Compare prediction success
nearestCentroidPredictor
Nearest centroid predictor
qvalue.restricted
qvalue convenience wrapper
plotNetworkHeatmap
Network heatmap plot
simulateEigengeneNetwork
Simulate eigengene network from a causal model
sizeGrWindow
Opens a graphics window with specified dimensions
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
goodSamples
Filter samples with too many missing entries
vectorTOM
Topological overlap for a subset of the whole set of genes
simulateMultiExpr
Simulate multi-set expression data
removePrincipalComponents
Remove leading principal components from data
propVarExplained
Proportion of variance explained by eigengenes.
verboseIplot
Scatterplot with density
moduleEigengenes
Calculate module eigengenes.
plotMat
Red and Green Color Image of Data Matrix
lowerTri2matrix
Reconstruct a symmetric matrix from a distance (lower-triangular) representation
unsignedAdjacency
Calculation of unsigned adjacency
simulateSmallLayer
Simulate small modules
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
simulateModule
Simulate a gene co-expression module
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
verboseScatterplot
Scatterplot annotated by regression line and p-value
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
subsetTOM
Topological overlap for a subset of a whole set of genes
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
scaleFreePlot
Visual check of scale-free topology
setCorrelationPreservation
Summary correlation preservation measure
signedKME
Signed eigengene-based connectivity
greenWhiteRed
Green-white-red color sequence
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
redWhiteGreen
Red-white-green color sequence
plotMEpairs
Pairwise scatterplots of eigengenes
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
preservationNetworkConnectivity
Network preservation calculations
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
standardScreeningNumericTrait
Standard screening for numeric traits
rgcolors.func
Red and Green Color Specification
spaste
Space-less paste
stdErr
Standard error of the mean of a given vector.
plotCor
Red and Green Color Image of Correlation Matrix
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
addErrorBars
Add error bars to a barplot.
addGrid
Add grid lines to an existing plot.
corAndPvalue
Calculation of correlations and associated p-values
matchLabels
Relabel module labels to best match the given reference labels
randIndex
Rand index of two partitions
goodGenesMS
Filter genes with too many missing entries across multiple sets