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WGCNA (version 1.22)
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
1.22
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
June 19th, 2012
Functions in WGCNA (1.22)
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TrueTrait
Estimate the true trait underlying a list of surrogate markers.
BloodLists
Blood Cell Types with Corresponding Gene Markers
blockwiseModules
Automatic network construction and module detection
bicor
Biweight Midcorrelation
adjacency.polyReg
Adjacency matrix based on polynomial regression
adjacency
Calculate network adjacency
checkAdjMat
Check adjacency matrix
allowWGCNAThreads
Allow and disable multi-threading for certain WGCNA calculations
chooseTopHubInEachModule
Chooses the top hub gene in each module
addErrorBars
Add error bars to a barplot.
consensusKME
Calculate consensus kME (eigengene-based connectivities) across multiple data sets.
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
TOMsimilarityFromExpr
Topological overlap matrix
alignExpr
Align expression data with given vector
coClustering.permutationTest
Permutation test for co-clustering
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
blueWhiteRed
Blue-white-red color sequence
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
corPvalueStudent
Student asymptotic p-value for correlation
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
collectGarbage
Iterative garbage collection.
blockwiseConsensusModules
Find consensus modules across several datasets.
corPredictionSuccess
Qunatification of success of gene screening
exportNetworkToCytoscape
Export network to Cytoscape
BrainLists
Brain-Related Categories with Corresponding Gene Markers
SCsLists
Stem Cell-Related Genes with Corresponding Gene Markers
goodGenes
Filter genes with too many missing entries
addTraitToMEs
Add trait information to multi-set module eigengene structure
cor
Fast calculations of Pearson correlation.
checkSets
Check structure and retrieve sizes of a group of datasets.
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
addGrid
Add grid lines to an existing plot.
blockwiseIndividualTOMs
Calculation of block-wise topological overlaps
GTOMdist
Generalized Topological Overlap Measure
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
coClustering
Co-clustering measure of cluster preservation between two clusterings
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
mergeCloseModules
Merge close modules in gene expression data
labeledBarplot
Barplot with text or color labels.
moduleEigengenes
Calculate module eigengenes.
WGCNA-package
Weighted Gene Co-Expression Network Analysis
cutreeStaticColor
Constant height tree cut using color labels
labeledHeatmap
Produce a labeled heatmap plot
matrixToNetwork
Construct a network from a matrix
TOMplot
Graphical representation of the Topological Overlap Matrix
labelPoints
Label scatterplot points
plotDendroAndColors
Dendrogram plot with color annotation of objects
cutreeStatic
Constant-height tree cut
corAndPvalue
Calculation of correlations and associated p-values
correlationPreservation
Preservation of eigengene correlations
keepCommonProbes
Keep probes that are shared among given data sets
exportNetworkToVisANT
Export network data in format readable by VisANT
intramodularConnectivity
Calculation of intramodular connectivity
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
simulateModule
Simulate a gene co-expression module
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
scaleFreePlot
Visual check of scale-free topology
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
networkConcepts
Calculations of network concepts
projectiveKMeans
Projective K-means (pre-)clustering of expression data
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
signedKME
Signed eigengene-based connectivity
goodSamples
Filter samples with too many missing entries
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
removePrincipalComponents
Remove leading principal components from data
metaZfunction
Meta-analysis Z statistic
modulePreservation
Calculation of module preservation statistics
displayColors
Show colors used to label modules
randIndex
Rand index of two partitions
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
goodGenesMS
Filter genes with too many missing entries across multiple sets
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
multiSetMEs
Calculate module eigengenes.
greenBlackRed
Green-black-red color sequence
moduleNumber
Fixed-height cut of a dendrogram.
simulateMultiExpr
Simulate multi-set expression data
qvalue
Estimate the q-values for a given set of p-values
simulateDatExpr
Simulation of expression data
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
fixDataStructure
Put single-set data into a form useful for multiset calculations.
spaste
Space-less paste
labels2colors
Convert numerical labels to colors.
metaAnalysis
Meta-analysis of binary and continuous variables
Inline display of progress
Inline display of progress
colQuantileC
Fast colunm-wise quantile of a matrix.
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
collapseRows
Select one representative row per group
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
propVarExplained
Proportion of variance explained by eigengenes.
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
lowerTri2matrix
Reconstruct a symmetric matrix from a distance (lower-triangular) representation
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
standardScreeningNumericTrait
Standard screening for numeric traits
plotMat
Red and Green Color Image of Data Matrix
stat.bwss
Between and Within Group Sum of Squares Calculation
greenWhiteRed
Green-white-red color sequence
prepComma
Prepend a comma to a non-empty string
nPresent
Number of present data entries.
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
plotColorUnderTree
Plot color rows under a dendrogram
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
rgcolors.func
Red and Green Color Specification
preservationNetworkConnectivity
Network preservation calculations
hubGeneSignificance
Hubgene significance
stdErr
Standard error of the mean of a given vector.
nSets
Number of sets in a multi-set variable
vectorTOM
Topological overlap for a subset of the whole set of genes
plotModuleSignificance
Barplot of module significance
plotMEpairs
Pairwise scatterplots of eigengenes
simulateSmallLayer
Simulate small modules
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
setCorrelationPreservation
Summary correlation preservation measure
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
orderMEs
Put close eigenvectors next to each other
stat.diag.da
Diagonal Discriminant Analysis
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
qvalue.restricted
qvalue convenience wrapper
collapseRowsUsingKME
Selects one representative row per group based on kME
pquantile
Parallel quantile, median, mean
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
simulateEigengeneNetwork
Simulate eigengene network from a causal model
verboseIplot
Scatterplot with density
sizeGrWindow
Opens a graphics window with specified dimensions
votingLinearPredictor
Voting linear predictor
redWhiteGreen
Red-white-green color sequence
plotNetworkHeatmap
Network heatmap plot
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix.
standardColors
Colors this library uses for labeling modules.
dynamicMergeCut
Threshold for module merging
signumAdjacencyFunction
Hard-thresholding adjacency function
verboseScatterplot
Scatterplot annotated by regression line and p-value
stratifiedBarplot
Bar plots of data across two splitting parameters
subsetTOM
Topological overlap for a subset of a whole set of genes
networkScreeningGS
Network gene screening with an external gene significance measure
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
networkScreening
Identification of genes related to a trait
plotCor
Red and Green Color Image of Correlation Matrix
softConnectivity
Calculates connectivity of a weighted network.
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
corPvalueFisher
Fisher's asymptotic p-value for correlation
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
overlapTable
Calculate overlap of modules
standardScreeningBinaryTrait
Standard screening for binatry traits
unsignedAdjacency
Calculation of unsigned adjacency
userListEnrichment
Measure enrichment between inputted and user-defined lists
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
chooseOneHubInEachModule
Chooses a single hub gene in each module
multiData.eigengeneSignificance
Eigengene significance across multiple sets
numbers2colors
Color representation for a numeric variable
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
simulateDatExpr5Modules
Simplified simulation of expression data
automaticNetworkScreening
One-step automatic network gene screening
clusterCoef
Clustering coefficient calculation
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
na
Basic Statistical Functions for Handling Missing Values
moduleMergeUsingKME
Merge modules and reassign genes using kME.
nearestCentroidPredictor
Nearest centroid predictor
matchLabels
Relabel module labels to best match the given reference labels
normalizeLabels
Transform numerical labels into normal order.
plotEigengeneNetworks
Eigengene network plot
relativeCorPredictionSuccess
Compare prediction success