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WGCNA (version 1.19)
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
1.19
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
March 3rd, 2012
Functions in WGCNA (1.19)
Search functions
collapseRowsUsingKME
Selects one representative row per group based on kME
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
corPredictionSuccess
Qunatification of success of gene screening
GTOMdist
Generalized Topological Overlap Measure
cutreeStaticColor
Constant height tree cut using color labels
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
addTraitToMEs
Add trait information to multi-set module eigengene structure
colQuantileC
Fast colunm-wise quantile of a matrix.
addErrorBars
Add error bars to a barplot.
coClustering.permutationTest
Permutation test for co-clustering
chooseTopHubInEachModule
Chooses the top hub gene in each module
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
goodSamples
Filter samples with too many missing entries
dynamicMergeCut
Threshold for module merging
matchLabels
Relabel module labels to best match the given reference labels
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
collapseRows
Select one representative row per group
checkSets
Check structure and retrieve sizes of a group of datasets.
automaticNetworkScreening
One-step automatic network gene screening
corPvalueFisher
Fisher's asymptotic p-value for correlation
consensusKME
Calculate consensus kME (eigengene-based connectivities) across multiple data sets.
cor
Fast calculations of Pearson correlation.
numbers2colors
Color representation for a numeric variable
moduleNumber
Fixed-height cut of a dendrogram.
correlationPreservation
Preservation of eigengene correlations
propVarExplained
Proportion of variance explained by eigengenes.
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
addGrid
Add grid lines to an existing plot.
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
corPvalueStudent
Student asymptotic p-value for correlation
chooseOneHubInEachModule
Chooses a single hub gene in each module
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
TOMplot
Graphical representation of the Topological Overlap Matrix
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
labeledBarplot
Barplot with text or color labels.
projectiveKMeans
Projective K-means (pre-)clustering of expression data
Inline display of progress
Inline display of progress
clusterCoef
Clustering coefficient calculation
labeledHeatmap
Produce a labeled heatmap plot
blockwiseConsensusModules
Find consensus modules across several datasets.
SCsLists
Stem Cell-Related Genes with Corresponding Gene Markers
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
exportNetworkToCytoscape
Export network to Cytoscape
keepCommonProbes
Keep probes that are shared among given data sets
networkScreening
Identification of genes related to a trait
stratifiedBarplot
Bar plots of data across two splitting parameters
plotDendroAndColors
Dendrogram plot with color annotation of objects
corAndPvalue
Calculation of correlations and associated p-values
labelPoints
Label scatterplot points
lowerTri2matrix
Reconstruct a symmetric matrix from a distance (lower-triangular) representation
pquantile
Parallel quantile, median, mean
labels2colors
Convert numerical labels to colors.
plotNetworkHeatmap
Network heatmap plot
mergeCloseModules
Merge close modules in gene expression data
plotColorUnderTree
Plot color rows under a dendrogram
moduleMergeUsingKME
Merge modules and reassign genes using kME.
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
coClustering
Co-clustering measure of cluster preservation between two clusterings
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
TrueTrait
Estimate the true trait underlying a list of surrogate markers.
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
TOMsimilarityFromExpr
Topological overlap matrix
adjacency
Calculate network adjacency
relativeCorPredictionSuccess
Compare prediction success
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
nearestCentroidPredictor
Nearest centroid predictor
matrixToNetwork
Construct a network from a matrix
nPresent
Number of present data entries.
allowWGCNAThreads
Allow and disable multi-threading for certain WGCNA calculations
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
adjacency.polyReg
Adjacency matrix based on polynomial regression
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
networkConcepts
Calculations of network concepts
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
randIndex
Rand index of two partitions
bicor
Biweight Midcorrelation
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix.
scaleFreePlot
Visual check of scale-free topology
greenBlackRed
Green-black-red color sequence
WGCNA-package
Weighted Gene Co-Expression Network Analysis
vectorTOM
Topological overlap for a subset of the whole set of genes
overlapTable
Calculate overlap of modules
exportNetworkToVisANT
Export network data in format readable by VisANT
cutreeStatic
Constant-height tree cut
standardScreeningNumericTrait
Standard screening for numeric traits
goodGenes
Filter genes with too many missing entries
moduleEigengenes
Calculate module eigengenes.
greenWhiteRed
Green-white-red color sequence
fixDataStructure
Put single-set data into a form useful for multiset calculations.
hubGeneSignificance
Hubgene significance
metaAnalysis
Meta-analysis of binary and continuous variables
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
blockwiseIndividualTOMs
Calculation of block-wise topological overlaps
checkAdjMat
Check adjacency matrix
displayColors
Show colors used to label modules
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
plotEigengeneNetworks
Eigengene network plot
simulateModule
Simulate a gene co-expression module
multiSetMEs
Calculate module eigengenes.
simulateSmallLayer
Simulate small modules
rgcolors.func
Red and Green Color Specification
modulePreservation
Calculation of module preservation statistics
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
userListEnrichment
Measure enrichment between inputted and user-defined lists
prepComma
Prepend a comma to a non-empty string
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
redWhiteGreen
Red-white-green color sequence
stdErr
Standard error of the mean of a given vector.
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
na
Basic Statistical Functions for Handling Missing Values
goodGenesMS
Filter genes with too many missing entries across multiple sets
intramodularConnectivity
Calculation of intramodular connectivity
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
alignExpr
Align expression data with given vector
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
qvalue.restricted
qvalue convenience wrapper
sizeGrWindow
Opens a graphics window with specified dimensions
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
standardScreeningBinaryTrait
Standard screening for binatry traits
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
unsignedAdjacency
Calculation of unsigned adjacency
metaZfunction
Meta-analysis Z statistic
simulateEigengeneNetwork
Simulate eigengene network from a causal model
votingLinearPredictor
Voting linear predictor
plotCor
Red and Green Color Image of Correlation Matrix
setCorrelationPreservation
Summary correlation preservation measure
plotMat
Red and Green Color Image of Data Matrix
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
signumAdjacencyFunction
Hard-thresholding adjacency function
networkScreeningGS
Network gene screening with an external gene significance measure
verboseIplot
Scatterplot with density
plotMEpairs
Pairwise scatterplots of eigengenes
simulateDatExpr5Modules
Simplified simulation of expression data
signedKME
Signed eigengene-based connectivity
plotModuleSignificance
Barplot of module significance
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
softConnectivity
Calculates connectivity of a weighted network.
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
preservationNetworkConnectivity
Network preservation calculations
removePrincipalComponents
Remove leading principal components from data
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
verboseScatterplot
Scatterplot annotated by regression line and p-value
normalizeLabels
Transform numerical labels into normal order.
nSets
Number of sets in a multi-set variable
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
orderMEs
Put close eigenvectors next to each other
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
spaste
Space-less paste
blockwiseModules
Automatic network construction and module detection
qvalue
Estimate the q-values for a given set of p-values
simulateMultiExpr
Simulate multi-set expression data
standardColors
Colors this library uses for labeling modules.
multiData.eigengeneSignificance
Eigengene significance across multiple sets
simulateDatExpr
Simulation of expression data
stat.diag.da
Diagonal Discriminant Analysis
stat.bwss
Between and Within Group Sum of Squares Calculation
subsetTOM
Topological overlap for a subset of a whole set of genes
BloodLists
Blood Cell Types with Corresponding Gene Markers
BrainLists
Brain-Related Categories with Corresponding Gene Markers
collectGarbage
Iterative garbage collection.
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.