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WGCNA (version 1.12)
Weighted Gene Co-Expression Network Analysis
Description
Functions necessary to perform Weighted Gene Co-Expression Network Analysis
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Install
install.packages('WGCNA')
Monthly Downloads
18,389
Version
1.12
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
August 17th, 2011
Functions in WGCNA (1.12)
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addGrid
Add grid lines to an existing plot.
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
BloodLists
Blood Cell Types with Corresponding Gene Markers
collectGarbage
Iterative garbage collection.
cutreeStatic
Constant-height tree cut
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
clusterCoef
Clustering coefficient calculation
coClustering
Co-clustering measure of cluster preservation between two clusterings
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
displayColors
Show colors used to label modules
mergeCloseModules
Merge close modules in gene expression data
coClustering.permutationTest
Permutation test for co-clustering
pquantile
Parallel quantile, median, mean
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
fixDataStructure
Put single-set data into a form useful for multiset calculations.
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
checkAdjMat
Check adjacency matrix
automaticNetworkScreening
One-step automatic network gene screening
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
alignExpr
Align expression data with given vector
goodGenes
Filter genes with too many missing entries
setCorrelationPreservation
Summary correlation preservation measure
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
corPvalueStudent
Student asymptotic p-value for correlation
TOMplot
Graphical representation of the Topological Overlap Matrix
moduleNumber
Fixed-height cut of a dendrogram.
simulateDatExpr
Simulation of expression data
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
cutreeStaticColor
Constant height tree cut using color labels
matchLabels
Relabel module labels to best match the given reference labels
greenWhiteRed
Green-white-red color sequence
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
simulateEigengeneNetwork
Simulate eigengene network from a causal model
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
numbers2colors
Color representation for a numeric variable
keepCommonProbes
Keep probes that are shared among given data sets
plotMat
Red and Green Color Image of Data Matrix
dynamicMergeCut
Threshold for module merging
stat.bwss
Between and Within Group Sum of Squares Calculation
signedKME
Signed eigengene-based connectivity
multiSetMEs
Calculate module eigengenes.
verboseScatterplot
Scatterplot annotated by regression line and p-value
randIndex
Rand index of two partitions
stat.diag.da
Diagonal Discriminant Analysis
normalizeLabels
Transform numerical labels into normal order.
corPredictionSuccess
Qunatification of success of gene screening
exportNetworkToCytoscape
Export network to Cytoscape
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
userListEnrichment
Measure enrichment between inputted and user-defined lists
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
sizeGrWindow
Opens a graphics window with specified dimensions
propVarExplained
Proportion of variance explained by eigengenes.
labeledBarplot
Barplot with text or color labels.
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
orderMEs
Put close eigenvectors next to each other
stdErr
Standard error of the mean of a given vector.
corPvalueFisher
Fisher's asymptotic p-value for correlation
collapseRows
Select one representative row per group
blockwiseConsensusModules
Find consensus modules across several datasets.
addTraitToMEs
Add trait information to multi-set module eigengene structure
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
labeledHeatmap
Produce a labeled heatmap plot
nPresent
Number of present data entries.
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
plotDendroAndColors
Dendrogram plot with color annotation of objects
BrainLists
Brain-Related Categories with Corresponding Gene Markers
colQuantileC
Fast colunm-wise quantile of a matrix.
prepComma
Prepend a comma to a non-empty string
Inline display of progress
Inline display of progress
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
modulePreservation
Calculation of module preservation statistics
nearestCentroidPredictor
Nearest centroid predictor
redWhiteGreen
Red-white-green color sequence
removePrincipalComponents
Remove leading principal components from data
networkScreeningGS
Network gene screening with an external gene significance measure
addErrorBars
Add error bars to a barplot.
overlapTable
Calculate overlap of modules
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
stratifiedBarplot
Bar plots of data across two splitting parameters
correlationPreservation
Preservation of eigengene correlations
chooseOneHubInEachModule
Chooses a single hub gene in each module
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
simulateMultiExpr
Simulate multi-set expression data
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
standardScreeningNumericTrait
Standard screening for numeric traits
WGCNA-package
Weighted Gene Co-Expression Network Analysis
hubGeneSignificance
Hubgene significance
votingLinearPredictor
Voting linear predictor
GTOMdist
Generalized Topological Overlap Measure
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
goodGenesMS
Filter genes with too many missing entries across multiple sets
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
checkSets
Check structure and retrieve sizes of a group of datasets.
blockwiseModules
Automatic network construction and module detection
chooseTopHubInEachModule
Chooses the top hub gene in each module
moduleMergeUsingKME
Merge modules and reassign genes using kME.
greenBlackRed
Green-black-red color sequence
intramodularConnectivity
Calculation of intramodular connectivity
moduleEigengenes
Calculate module eigengenes.
exportNetworkToVisANT
Export network data in format readable by VisANT
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
na
Basic Statistical Functions for Handling Missing Values
relativeCorPredictionSuccess
Compare prediction success
plotNetworkHeatmap
Network heatmap plot
plotEigengeneNetworks
Eigengene network plot
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
simulateSmallLayer
Simulate small modules
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
goodSamples
Filter samples with too many missing entries
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix.
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
networkConcepts
Calculations of network concepts
matrixToNetwork
Construct a network from a matrix
metaZfunction
Meta-analysis Z statistic
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
bicor
Biweight Midcorrelation
projectiveKMeans
Projective K-means (pre-)clustering of expression data
softConnectivity
Calculates connectivity of a weighted network.
plotCor
Red and Green Color Image of Correlation Matrix
plotModuleSignificance
Barplot of module significance
simulateModule
Simulate a gene co-expression module
rgcolors.func
Red and Green Color Specification
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
scaleFreePlot
Visual check of scale-free topology
standardColors
Colors this library uses for labeling modules.
TOMsimilarityFromExpr
Topological overlap matrix
adjacency.polyReg
Adjacency matrix based on polynomial regression
cor
Fast calculations of Pearson correlation.
plotMEpairs
Pairwise scatterplots of eigengenes
standardScreeningBinaryTrait
Standard screening for binatry traits
vectorTOM
Topological overlap for a subset of the whole set of genes
signumAdjacencyFunction
Hard-thresholding adjacency function
collapseRowsUsingKME
Selects one representative row per group based on kME
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
preservationNetworkConnectivity
Network preservation calculations
qvalue
Estimate the q-values for a given set of p-values
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
spaste
Space-less paste
simulateDatExpr5Modules
Simplified simulation of expression data
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
adjacency
Calculate network adjacency
corAndPvalue
Calculation of correlations and associated p-values
labels2colors
Convert numerical labels to colors.
networkScreening
Identification of genes related to a trait
plotColorUnderTree
Plot color rows under a dendrogram
subsetTOM
Topological overlap for a subset of a whole set of genes
unsignedAdjacency
Calculation of unsigned adjacency
labelPoints
Label scatterplot points