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WGCNA (version 1.11-1)
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
1.11-1
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
June 1st, 2011
Functions in WGCNA (1.11-1)
Search functions
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
BloodLists
Blood Cell Types with Corresponding Gene Markers
BrainLists
Brain-Related Categories with Corresponding Gene Markers
addErrorBars
Add error bars to a barplot.
cutreeStatic
Constant-height tree cut
collectGarbage
Iterative garbage collection.
labelPoints
Label scatterplot points
projectiveKMeans
Projective K-means (pre-)clustering of expression data
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
colQuantileC
Fast colunm-wise quantile of a matrix.
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
moduleMergeUsingKME
Merge modules and reassign genes using kME.
TOMsimilarityFromExpr
Topological overlap matrix
chooseTopHubInEachModule
Chooses the top hub gene in each module
automaticNetworkScreening
One-step automatic network gene screening
goodGenesMS
Filter genes with too many missing entries across multiple sets
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
dynamicMergeCut
Threshold for module merging
modulePreservation
Calculation of module preservation statistics
Inline display of progress
Inline display of progress
vectorTOM
Topological overlap for a subset of the whole set of genes
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
matchLabels
Relabel module labels to best match the given reference labels
labeledHeatmap
Produce a labeled heatmap plot
subsetTOM
Topological overlap for a subset of a whole set of genes
signumAdjacencyFunction
Hard-thresholding adjacency function
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
standardScreeningBinaryTrait
Standard screening for binatry traits
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
matrixToNetwork
Construct a network from a matrix
networkConcepts
Calculations of network concepts
preservationNetworkConnectivity
Network preservation calculations
stratifiedBarplot
Bar plots of data across two splitting parameters
adjacency.polyReg
Adjacency matrix based on polynomial regression
moduleEigengenes
Calculate module eigengenes.
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
nPresent
Number of present data entries.
blockwiseConsensusModules
Find consensus modules across several datasets.
adjacency
Calculate network adjacency
corPvalueFisher
Fisher's asymptotic p-value for correlation
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
plotModuleSignificance
Barplot of module significance
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
cor
Fast calculations of Pearson correlation.
cutreeStaticColor
Constant height tree cut using color labels
plot.mat
Red and Green Color Image of Data Matrix
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
alignExpr
Align expression data with given vector
signedKME
Signed eigengene-based connectivity
clusterCoef
Clustering coefficient calculation
plotColorUnderTree
Plot color rows under a dendrogram
setCorrelationPreservation
Summary correlation preservation measure
moduleNumber
Fixed-height cut of a dendrogram.
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
randIndex
Rand index of two partitions
unsignedAdjacency
Calculation of unsigned adjacency
coClustering.permutationTest
Permutation test for co-clustering
labeledBarplot
Barplot with text or color labels.
hubGeneSignificance
Hubgene significance
standardScreeningNumericTrait
Standard screening for numeric traits
WGCNA-package
Weighted Gene Co-Expression Network Analysis
exportNetworkToCytoscape
Export network to Cytoscape
TOMplot
Graphical representation of the Topological Overlap Matrix
stat.bwss
Between and Within Group Sum of Squares Calculation
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
labels2colors
Convert numerical labels to colors.
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix.
prepComma
Prepend a comma to a non-empty string
nearestCentroidPredictor
Nearest centroid predictor
mergeCloseModules
Merge close modules in gene expression data
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
checkAdjMat
Check adjacency matrix
corPredictionSuccess
Qunatification of success of gene screening
bicor
Biweight Midcorrelation
correlationPreservation
Preservation of eigengene correlations
displayColors
Show colors used to label modules
plotNetworkHeatmap
Network heatmap plot
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
standardColors
Colors this library uses for labeling modules.
rgcolors.func
Red and Green Color Specification
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
coClustering
Co-clustering measure of cluster preservation between two clusterings
networkScreening
Identification of genes related to a trait
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
networkScreeningGS
Network gene screening with an external gene significance measure
exportNetworkToVisANT
Export network data in format readable by VisANT
orderMEs
Put close eigenvectors next to each other
pquantile
Parallel quantile, median, mean
softConnectivity
Calculates connectivity of a weighted network.
stdErr
Standard error of the mean of a given vector.
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
collapseRows
Select one representative row per group
goodSamples
Filter samples with too many missing entries
intramodularConnectivity
Calculation of intramodular connectivity
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
keepCommonProbes
Keep probes that are shared among given data sets
greenBlackRed
Green-black-red color sequence
votingLinearPredictor
Voting linear predictor
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
simulateModule
Simulate a gene co-expression module
propVarExplained
Proportion of variance explained by eigengenes.
plotEigengeneNetworks
Eigengene network plot
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
fixDataStructure
Put single-set data into a form useful for multiset calculations.
collapseRowsUsingKME
Selects one representative row per group based on kME
stat.diag.da
Diagonal Discriminant Analysis
chooseOneHubInEachModule
Chooses a single hub gene in each module
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
plotDendroAndColors
Dendrogram plot with color annotation of objects
numbers2colors
Color representation for a numeric variable
qvalue
Estimate the q-values for a given set of p-values
relativeCorPredictionSuccess
Compare prediction success
metaZfunction
Meta-analysis Z statistic
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
removePrincipalComponents
Remove leading principal components from data
simulateMultiExpr
Simulate multi-set expression data
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
overlapTable
Calculate overlap of modules
spaste
Space-less paste
simulateDatExpr
Simulation of expression data
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
normalizeLabels
Transform numerical labels into normal order.
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
simulateDatExpr5Modules
Simplified simulation of expression data
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
scaleFreePlot
Visual check of scale-free topology
corAndPvalue
Calculation of correlations and associated p-values
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
goodGenes
Filter genes with too many missing entries
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
corPvalueStudent
Student asymptotic p-value for correlation
na
Basic Statistical Functions for Handling Missing Values
multiSetMEs
Calculate module eigengenes.
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
plotMEpairs
Pairwise scatterplots of eigengenes
sizeGrWindow
Opens a graphics window with specified dimensions
verboseScatterplot
Scatterplot annotated by regression line and p-value
GTOMdist
Generalized Topological Overlap Measure
addTraitToMEs
Add trait information to multi-set module eigengene structure
blockwiseModules
Automatic network construction and module detection
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
redWhiteGreen
Red-white-green color sequence
simulateSmallLayer
Simulate small modules
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
addGrid
Add grid lines to an existing plot.
checkSets
Check structure and retrieve sizes of a group of datasets.
greenWhiteRed
Green-white-red color sequence
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
plot.cor
Red and Green Color Image of Correlation Matrix
simulateEigengeneNetwork
Simulate eigengene network from a causal model
userListEnrichment
Measure enrichment between inputted and user-defined lists