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WGCNA (version 1.18-2)
Weighted Correlation Network Analysis
Description
Functions necessary to perform Weighted Correlation Network Analysis
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Install
install.packages('WGCNA')
Monthly Downloads
14,709
Version
1.18-2
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
January 13th, 2012
Functions in WGCNA (1.18-2)
Search functions
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
alignExpr
Align expression data with given vector
addErrorBars
Add error bars to a barplot.
SCsLists
Stem Cell-Related Genes with Corresponding Gene Markers
GTOMdist
Generalized Topological Overlap Measure
TOMsimilarityFromExpr
Topological overlap matrix
addTraitToMEs
Add trait information to multi-set module eigengene structure
blockwiseModules
Automatic network construction and module detection
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
addGrid
Add grid lines to an existing plot.
allowWGCNAThreads
Allow and disable multi-threading for certain WGCNA calculations
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix.
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
coClustering
Co-clustering measure of cluster preservation between two clusterings
TOMplot
Graphical representation of the Topological Overlap Matrix
adjacency
Calculate network adjacency
consensusKME
Calculate consensus kME (eigengene-based connectivities) across multiple data sets.
corPredictionSuccess
Qunatification of success of gene screening
collapseRows
Select one representative row per group
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
automaticNetworkScreening
One-step automatic network gene screening
bicor
Biweight Midcorrelation
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
chooseOneHubInEachModule
Chooses a single hub gene in each module
exportNetworkToCytoscape
Export network to Cytoscape
adjacency.polyReg
Adjacency matrix based on polynomial regression
goodGenesMS
Filter genes with too many missing entries across multiple sets
multiData.eigengeneSignificance
Eigengene significance across multiple sets
corPvalueStudent
Student asymptotic p-value for correlation
metaZfunction
Meta-analysis Z statistic
greenWhiteRed
Green-white-red color sequence
hubGeneSignificance
Hubgene significance
plotEigengeneNetworks
Eigengene network plot
checkSets
Check structure and retrieve sizes of a group of datasets.
na
Basic Statistical Functions for Handling Missing Values
BrainLists
Brain-Related Categories with Corresponding Gene Markers
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
collectGarbage
Iterative garbage collection.
clusterCoef
Clustering coefficient calculation
WGCNA-package
Weighted Gene Co-Expression Network Analysis
labelPoints
Label scatterplot points
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
BloodLists
Blood Cell Types with Corresponding Gene Markers
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
corAndPvalue
Calculation of correlations and associated p-values
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
fixDataStructure
Put single-set data into a form useful for multiset calculations.
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
coClustering.permutationTest
Permutation test for co-clustering
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
checkAdjMat
Check adjacency matrix
mergeCloseModules
Merge close modules in gene expression data
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
normalizeLabels
Transform numerical labels into normal order.
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
corPvalueFisher
Fisher's asymptotic p-value for correlation
blockwiseConsensusModules
Find consensus modules across several datasets.
setCorrelationPreservation
Summary correlation preservation measure
relativeCorPredictionSuccess
Compare prediction success
metaAnalysis
Meta-analysis of binary and continuous variables
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
chooseTopHubInEachModule
Chooses the top hub gene in each module
cutreeStaticColor
Constant height tree cut using color labels
spaste
Space-less paste
plotDendroAndColors
Dendrogram plot with color annotation of objects
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
cutreeStatic
Constant-height tree cut
exportNetworkToVisANT
Export network data in format readable by VisANT
labeledBarplot
Barplot with text or color labels.
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
keepCommonProbes
Keep probes that are shared among given data sets
goodSamples
Filter samples with too many missing entries
Inline display of progress
Inline display of progress
multiSetMEs
Calculate module eigengenes.
matrixToNetwork
Construct a network from a matrix
projectiveKMeans
Projective K-means (pre-)clustering of expression data
greenBlackRed
Green-black-red color sequence
colQuantileC
Fast colunm-wise quantile of a matrix.
preservationNetworkConnectivity
Network preservation calculations
displayColors
Show colors used to label modules
labels2colors
Convert numerical labels to colors.
plotColorUnderTree
Plot color rows under a dendrogram
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
intramodularConnectivity
Calculation of intramodular connectivity
sizeGrWindow
Opens a graphics window with specified dimensions
networkScreeningGS
Network gene screening with an external gene significance measure
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
signedKME
Signed eigengene-based connectivity
matchLabels
Relabel module labels to best match the given reference labels
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
modulePreservation
Calculation of module preservation statistics
overlapTable
Calculate overlap of modules
qvalue
Estimate the q-values for a given set of p-values
plotModuleSignificance
Barplot of module significance
propVarExplained
Proportion of variance explained by eigengenes.
userListEnrichment
Measure enrichment between inputted and user-defined lists
collapseRowsUsingKME
Selects one representative row per group based on kME
subsetTOM
Topological overlap for a subset of a whole set of genes
correlationPreservation
Preservation of eigengene correlations
simulateModule
Simulate a gene co-expression module
simulateDatExpr
Simulation of expression data
moduleMergeUsingKME
Merge modules and reassign genes using kME.
verboseIplot
Scatterplot with density
simulateDatExpr5Modules
Simplified simulation of expression data
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
unsignedAdjacency
Calculation of unsigned adjacency
moduleEigengenes
Calculate module eigengenes.
plotCor
Red and Green Color Image of Correlation Matrix
nearestCentroidPredictor
Nearest centroid predictor
moduleNumber
Fixed-height cut of a dendrogram.
redWhiteGreen
Red-white-green color sequence
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
dynamicMergeCut
Threshold for module merging
simulateEigengeneNetwork
Simulate eigengene network from a causal model
stat.diag.da
Diagonal Discriminant Analysis
vectorTOM
Topological overlap for a subset of the whole set of genes
rgcolors.func
Red and Green Color Specification
stat.bwss
Between and Within Group Sum of Squares Calculation
networkConcepts
Calculations of network concepts
standardColors
Colors this library uses for labeling modules.
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
removePrincipalComponents
Remove leading principal components from data
numbers2colors
Color representation for a numeric variable
stdErr
Standard error of the mean of a given vector.
pquantile
Parallel quantile, median, mean
qvalue.restricted
qvalue convenience wrapper
simulateMultiExpr
Simulate multi-set expression data
networkScreening
Identification of genes related to a trait
randIndex
Rand index of two partitions
labeledHeatmap
Produce a labeled heatmap plot
nPresent
Number of present data entries.
verboseScatterplot
Scatterplot annotated by regression line and p-value
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
plotMEpairs
Pairwise scatterplots of eigengenes
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
votingLinearPredictor
Voting linear predictor
standardScreeningNumericTrait
Standard screening for numeric traits
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
plotNetworkHeatmap
Network heatmap plot
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
softConnectivity
Calculates connectivity of a weighted network.
orderMEs
Put close eigenvectors next to each other
prepComma
Prepend a comma to a non-empty string
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
stratifiedBarplot
Bar plots of data across two splitting parameters
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
plotMat
Red and Green Color Image of Data Matrix
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
signumAdjacencyFunction
Hard-thresholding adjacency function
cor
Fast calculations of Pearson correlation.
goodGenes
Filter genes with too many missing entries
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
simulateSmallLayer
Simulate small modules
standardScreeningBinaryTrait
Standard screening for binatry traits
scaleFreePlot
Visual check of scale-free topology