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WGCNA (version 1.18-1)
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
1.18-1
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
January 5th, 2012
Functions in WGCNA (1.18-1)
Search functions
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
BrainLists
Brain-Related Categories with Corresponding Gene Markers
GTOMdist
Generalized Topological Overlap Measure
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
allowWGCNAThreads
Allow and disable multi-threading for certain WGCNA calculations
cor
Fast calculations of Pearson correlation.
correlationPreservation
Preservation of eigengene correlations
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix.
blockwiseConsensusModules
Find consensus modules across several datasets.
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
metaZfunction
Meta-analysis Z statistic
displayColors
Show colors used to label modules
alignExpr
Align expression data with given vector
multiSetMEs
Calculate module eigengenes.
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
addGrid
Add grid lines to an existing plot.
collapseRowsUsingKME
Selects one representative row per group based on kME
chooseOneHubInEachModule
Chooses a single hub gene in each module
coClustering.permutationTest
Permutation test for co-clustering
plotDendroAndColors
Dendrogram plot with color annotation of objects
TOMplot
Graphical representation of the Topological Overlap Matrix
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
moduleNumber
Fixed-height cut of a dendrogram.
fixDataStructure
Put single-set data into a form useful for multiset calculations.
corPvalueFisher
Fisher's asymptotic p-value for correlation
adjacency
Calculate network adjacency
SCsLists
Stem Cell-Related Genes with Corresponding Gene Markers
addErrorBars
Add error bars to a barplot.
adjacency.polyReg
Adjacency matrix based on polynomial regression
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
bicor
Biweight Midcorrelation
multiData.eigengeneSignificance
Eigengene significance across multiple sets
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
dynamicMergeCut
Threshold for module merging
colQuantileC
Fast colunm-wise quantile of a matrix.
networkScreening
Identification of genes related to a trait
cutreeStaticColor
Constant height tree cut using color labels
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
collectGarbage
Iterative garbage collection.
numbers2colors
Color representation for a numeric variable
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
collapseRows
Select one representative row per group
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
checkSets
Check structure and retrieve sizes of a group of datasets.
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
plotModuleSignificance
Barplot of module significance
simulateDatExpr
Simulation of expression data
goodSamples
Filter samples with too many missing entries
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
plotColorUnderTree
Plot color rows under a dendrogram
blockwiseModules
Automatic network construction and module detection
cutreeStatic
Constant-height tree cut
hubGeneSignificance
Hubgene significance
chooseTopHubInEachModule
Chooses the top hub gene in each module
coClustering
Co-clustering measure of cluster preservation between two clusterings
TOMsimilarityFromExpr
Topological overlap matrix
automaticNetworkScreening
One-step automatic network gene screening
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
matrixToNetwork
Construct a network from a matrix
consensusKME
Calculate consensus kME (eigengene-based connectivities) across multiple data sets.
goodGenesMS
Filter genes with too many missing entries across multiple sets
plotCor
Red and Green Color Image of Correlation Matrix
intramodularConnectivity
Calculation of intramodular connectivity
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
redWhiteGreen
Red-white-green color sequence
corPredictionSuccess
Qunatification of success of gene screening
greenWhiteRed
Green-white-red color sequence
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
matchLabels
Relabel module labels to best match the given reference labels
projectiveKMeans
Projective K-means (pre-)clustering of expression data
labels2colors
Convert numerical labels to colors.
addTraitToMEs
Add trait information to multi-set module eigengene structure
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
checkAdjMat
Check adjacency matrix
orderMEs
Put close eigenvectors next to each other
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
standardScreeningNumericTrait
Standard screening for numeric traits
keepCommonProbes
Keep probes that are shared among given data sets
signumAdjacencyFunction
Hard-thresholding adjacency function
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
greenBlackRed
Green-black-red color sequence
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
exportNetworkToVisANT
Export network data in format readable by VisANT
goodGenes
Filter genes with too many missing entries
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
userListEnrichment
Measure enrichment between inputted and user-defined lists
spaste
Space-less paste
labeledHeatmap
Produce a labeled heatmap plot
plotNetworkHeatmap
Network heatmap plot
BloodLists
Blood Cell Types with Corresponding Gene Markers
WGCNA-package
Weighted Gene Co-Expression Network Analysis
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
corAndPvalue
Calculation of correlations and associated p-values
corPvalueStudent
Student asymptotic p-value for correlation
mergeCloseModules
Merge close modules in gene expression data
metaAnalysis
Meta-analysis of binary and continuous variables
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
plotEigengeneNetworks
Eigengene network plot
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
simulateDatExpr5Modules
Simplified simulation of expression data
propVarExplained
Proportion of variance explained by eigengenes.
networkScreeningGS
Network gene screening with an external gene significance measure
rgcolors.func
Red and Green Color Specification
standardScreeningBinaryTrait
Standard screening for binatry traits
qvalue.restricted
qvalue convenience wrapper
Inline display of progress
Inline display of progress
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
qvalue
Estimate the q-values for a given set of p-values
randIndex
Rand index of two partitions
labeledBarplot
Barplot with text or color labels.
labelPoints
Label scatterplot points
softConnectivity
Calculates connectivity of a weighted network.
nPresent
Number of present data entries.
plotMat
Red and Green Color Image of Data Matrix
preservationNetworkConnectivity
Network preservation calculations
stdErr
Standard error of the mean of a given vector.
relativeCorPredictionSuccess
Compare prediction success
prepComma
Prepend a comma to a non-empty string
simulateModule
Simulate a gene co-expression module
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
votingLinearPredictor
Voting linear predictor
verboseScatterplot
Scatterplot annotated by regression line and p-value
sizeGrWindow
Opens a graphics window with specified dimensions
networkConcepts
Calculations of network concepts
subsetTOM
Topological overlap for a subset of a whole set of genes
unsignedAdjacency
Calculation of unsigned adjacency
simulateEigengeneNetwork
Simulate eigengene network from a causal model
stat.diag.da
Diagonal Discriminant Analysis
simulateMultiExpr
Simulate multi-set expression data
stat.bwss
Between and Within Group Sum of Squares Calculation
exportNetworkToCytoscape
Export network to Cytoscape
stratifiedBarplot
Bar plots of data across two splitting parameters
vectorTOM
Topological overlap for a subset of the whole set of genes
overlapTable
Calculate overlap of modules
pquantile
Parallel quantile, median, mean
na
Basic Statistical Functions for Handling Missing Values
plotMEpairs
Pairwise scatterplots of eigengenes
moduleEigengenes
Calculate module eigengenes.
clusterCoef
Clustering coefficient calculation
scaleFreePlot
Visual check of scale-free topology
simulateSmallLayer
Simulate small modules
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
modulePreservation
Calculation of module preservation statistics
verboseIplot
Scatterplot with density
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
removePrincipalComponents
Remove leading principal components from data
setCorrelationPreservation
Summary correlation preservation measure
standardColors
Colors this library uses for labeling modules.
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
moduleMergeUsingKME
Merge modules and reassign genes using kME.
nearestCentroidPredictor
Nearest centroid predictor
normalizeLabels
Transform numerical labels into normal order.
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
signedKME
Signed eigengene-based connectivity