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WGCNA (version 1.11-3)
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
1.11-3
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
July 7th, 2011
Functions in WGCNA (1.11-3)
Search functions
correlationPreservation
Preservation of eigengene correlations
cutreeStatic
Constant-height tree cut
automaticNetworkScreening
One-step automatic network gene screening
matrixToNetwork
Construct a network from a matrix
clusterCoef
Clustering coefficient calculation
adjacency
Calculate network adjacency
preservationNetworkConnectivity
Network preservation calculations
mergeCloseModules
Merge close modules in gene expression data
checkAdjMat
Check adjacency matrix
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
alignExpr
Align expression data with given vector
plotNetworkHeatmap
Network heatmap plot
BloodLists
Blood Cell Types with Corresponding Gene Markers
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
addErrorBars
Add error bars to a barplot.
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
TOMplot
Graphical representation of the Topological Overlap Matrix
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
displayColors
Show colors used to label modules
addGrid
Add grid lines to an existing plot.
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix.
cutreeStaticColor
Constant height tree cut using color labels
BrainLists
Brain-Related Categories with Corresponding Gene Markers
pquantile
Parallel quantile, median, mean
adjacency.polyReg
Adjacency matrix based on polynomial regression
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
collapseRows
Select one representative row per group
projectiveKMeans
Projective K-means (pre-)clustering of expression data
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
coClustering
Co-clustering measure of cluster preservation between two clusterings
simulateDatExpr5Modules
Simplified simulation of expression data
propVarExplained
Proportion of variance explained by eigengenes.
corPvalueFisher
Fisher's asymptotic p-value for correlation
exportNetworkToVisANT
Export network data in format readable by VisANT
labels2colors
Convert numerical labels to colors.
dynamicMergeCut
Threshold for module merging
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
GTOMdist
Generalized Topological Overlap Measure
greenWhiteRed
Green-white-red color sequence
vectorTOM
Topological overlap for a subset of the whole set of genes
coClustering.permutationTest
Permutation test for co-clustering
chooseTopHubInEachModule
Chooses the top hub gene in each module
nPresent
Number of present data entries.
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
goodSamples
Filter samples with too many missing entries
standardScreeningNumericTrait
Standard screening for numeric traits
chooseOneHubInEachModule
Chooses a single hub gene in each module
addTraitToMEs
Add trait information to multi-set module eigengene structure
colQuantileC
Fast colunm-wise quantile of a matrix.
corAndPvalue
Calculation of correlations and associated p-values
labeledHeatmap
Produce a labeled heatmap plot
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
fixDataStructure
Put single-set data into a form useful for multiset calculations.
moduleNumber
Fixed-height cut of a dendrogram.
moduleEigengenes
Calculate module eigengenes.
collectGarbage
Iterative garbage collection.
modulePreservation
Calculation of module preservation statistics
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
metaZfunction
Meta-analysis Z statistic
orderMEs
Put close eigenvectors next to each other
multiSetMEs
Calculate module eigengenes.
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
userListEnrichment
Measure enrichment between inputted and user-defined lists
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
verboseScatterplot
Scatterplot annotated by regression line and p-value
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
na
Basic Statistical Functions for Handling Missing Values
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
plot.mat
Red and Green Color Image of Data Matrix
nearestCentroidPredictor
Nearest centroid predictor
plotMEpairs
Pairwise scatterplots of eigengenes
sizeGrWindow
Opens a graphics window with specified dimensions
TOMsimilarityFromExpr
Topological overlap matrix
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
simulateSmallLayer
Simulate small modules
redWhiteGreen
Red-white-green color sequence
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
checkSets
Check structure and retrieve sizes of a group of datasets.
randIndex
Rand index of two partitions
blockwiseModules
Automatic network construction and module detection
goodGenesMS
Filter genes with too many missing entries across multiple sets
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
labeledBarplot
Barplot with text or color labels.
plotEigengeneNetworks
Eigengene network plot
labelPoints
Label scatterplot points
signumAdjacencyFunction
Hard-thresholding adjacency function
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
intramodularConnectivity
Calculation of intramodular connectivity
networkScreening
Identification of genes related to a trait
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
normalizeLabels
Transform numerical labels into normal order.
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
bicor
Biweight Midcorrelation
stat.bwss
Between and Within Group Sum of Squares Calculation
collapseRowsUsingKME
Selects one representative row per group based on kME
numbers2colors
Color representation for a numeric variable
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
standardColors
Colors this library uses for labeling modules.
spaste
Space-less paste
networkScreeningGS
Network gene screening with an external gene significance measure
simulateEigengeneNetwork
Simulate eigengene network from a causal model
qvalue
Estimate the q-values for a given set of p-values
simulateModule
Simulate a gene co-expression module
matchLabels
Relabel module labels to best match the given reference labels
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
corPvalueStudent
Student asymptotic p-value for correlation
setCorrelationPreservation
Summary correlation preservation measure
signedKME
Signed eigengene-based connectivity
softConnectivity
Calculates connectivity of a weighted network.
stat.diag.da
Diagonal Discriminant Analysis
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
hubGeneSignificance
Hubgene significance
cor
Fast calculations of Pearson correlation.
networkConcepts
Calculations of network concepts
plotModuleSignificance
Barplot of module significance
stdErr
Standard error of the mean of a given vector.
standardScreeningBinaryTrait
Standard screening for binatry traits
Inline display of progress
Inline display of progress
goodGenes
Filter genes with too many missing entries
plotDendroAndColors
Dendrogram plot with color annotation of objects
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
votingLinearPredictor
Voting linear predictor
relativeCorPredictionSuccess
Compare prediction success
unsignedAdjacency
Calculation of unsigned adjacency
keepCommonProbes
Keep probes that are shared among given data sets
removePrincipalComponents
Remove leading principal components from data
greenBlackRed
Green-black-red color sequence
scaleFreePlot
Visual check of scale-free topology
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
overlapTable
Calculate overlap of modules
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
plot.cor
Red and Green Color Image of Correlation Matrix
moduleMergeUsingKME
Merge modules and reassign genes using kME.
plotColorUnderTree
Plot color rows under a dendrogram
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
simulateDatExpr
Simulation of expression data
simulateMultiExpr
Simulate multi-set expression data
corPredictionSuccess
Qunatification of success of gene screening
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
exportNetworkToCytoscape
Export network to Cytoscape
prepComma
Prepend a comma to a non-empty string
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
rgcolors.func
Red and Green Color Specification
subsetTOM
Topological overlap for a subset of a whole set of genes
WGCNA-package
Weighted Gene Co-Expression Network Analysis
blockwiseConsensusModules
Find consensus modules across several datasets.
stratifiedBarplot
Bar plots of data across two splitting parameters