RDocumentation
Moon
Learn R
Search all packages and functions
⚠️
There's a newer version (1.72-5) of this package.
Take me there.
WGCNA (version 1.15)
Weighted Correlation Network Analysis
Description
Functions necessary to perform Weighted Correlation Network Analysis
Copy Link
Copy
Link to current version
Version
Version
1.72-5
1.72-1
1.71
1.70-3
1.69
1.68
1.67
1.66
1.64-1
1.63
1.62
1.61
1.60
1.51
1.49
1.48
1.47
1.46
1.43
1.42
1.41-1
1.34
1.27-1
1.26
1.25-2
1.25-1
1.23-1
1.22
1.20
1.19
1.18-2
1.18-1
1.17
1.15
1.14
1.13
1.12
1.11-3
1.11-2
1.11-1
1.10-2
1.00
0.99
0.98
0.97
0.96
0.95
0.94
0.93
0.92-3
Down Chevron
Install
install.packages('WGCNA')
Monthly Downloads
18,389
Version
1.15
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
November 12th, 2011
Functions in WGCNA (1.15)
Search functions
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
coClustering
Co-clustering measure of cluster preservation between two clusterings
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
plotMat
Red and Green Color Image of Data Matrix
checkAdjMat
Check adjacency matrix
simulateDatExpr
Simulation of expression data
multiSetMEs
Calculate module eigengenes.
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
standardColors
Colors this library uses for labeling modules.
standardScreeningNumericTrait
Standard screening for numeric traits
coClustering.permutationTest
Permutation test for co-clustering
cor
Fast calculations of Pearson correlation.
nearestCentroidPredictor
Nearest centroid predictor
cutreeStatic
Constant-height tree cut
userListEnrichment
Measure enrichment between inputted and user-defined lists
displayColors
Show colors used to label modules
addTraitToMEs
Add trait information to multi-set module eigengene structure
colQuantileC
Fast colunm-wise quantile of a matrix.
softConnectivity
Calculates connectivity of a weighted network.
dynamicMergeCut
Threshold for module merging
SCsLists
Stem Cell-Related Genes with Corresponding Gene Markers
adjacency
Calculate network adjacency
corPredictionSuccess
Qunatification of success of gene screening
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix.
stdErr
Standard error of the mean of a given vector.
collapseRows
Select one representative row per group
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
goodSamples
Filter samples with too many missing entries
plotDendroAndColors
Dendrogram plot with color annotation of objects
collapseRowsUsingKME
Selects one representative row per group based on kME
unsignedAdjacency
Calculation of unsigned adjacency
nPresent
Number of present data entries.
collectGarbage
Iterative garbage collection.
metaAnalysis
Meta-analysis of binary and continuous variables
networkScreening
Identification of genes related to a trait
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
blockwiseModules
Automatic network construction and module detection
plotColorUnderTree
Plot color rows under a dendrogram
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
corAndPvalue
Calculation of correlations and associated p-values
exportNetworkToCytoscape
Export network to Cytoscape
normalizeLabels
Transform numerical labels into normal order.
chooseOneHubInEachModule
Chooses a single hub gene in each module
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
matchLabels
Relabel module labels to best match the given reference labels
plotEigengeneNetworks
Eigengene network plot
corPvalueFisher
Fisher's asymptotic p-value for correlation
verboseIplot
Scatterplot with density
standardScreeningBinaryTrait
Standard screening for binatry traits
signedKME
Signed eigengene-based connectivity
fixDataStructure
Put single-set data into a form useful for multiset calculations.
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
chooseTopHubInEachModule
Chooses the top hub gene in each module
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
BloodLists
Blood Cell Types with Corresponding Gene Markers
intramodularConnectivity
Calculation of intramodular connectivity
multiData.eigengeneSignificance
Eigengene significance across multiple sets
consensusKME
Calculate consensus kME (eigengene-based connectivities) across multiple data sets.
GTOMdist
Generalized Topological Overlap Measure
numbers2colors
Color representation for a numeric variable
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
vectorTOM
Topological overlap for a subset of the whole set of genes
stratifiedBarplot
Bar plots of data across two splitting parameters
modulePreservation
Calculation of module preservation statistics
labeledBarplot
Barplot with text or color labels.
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
moduleMergeUsingKME
Merge modules and reassign genes using kME.
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
plotCor
Red and Green Color Image of Correlation Matrix
TOMplot
Graphical representation of the Topological Overlap Matrix
WGCNA-package
Weighted Gene Co-Expression Network Analysis
blockwiseConsensusModules
Find consensus modules across several datasets.
plotNetworkHeatmap
Network heatmap plot
stat.bwss
Between and Within Group Sum of Squares Calculation
automaticNetworkScreening
One-step automatic network gene screening
hubGeneSignificance
Hubgene significance
TOMsimilarityFromExpr
Topological overlap matrix
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
propVarExplained
Proportion of variance explained by eigengenes.
greenWhiteRed
Green-white-red color sequence
overlapTable
Calculate overlap of modules
projectiveKMeans
Projective K-means (pre-)clustering of expression data
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
signumAdjacencyFunction
Hard-thresholding adjacency function
rgcolors.func
Red and Green Color Specification
checkSets
Check structure and retrieve sizes of a group of datasets.
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
BrainLists
Brain-Related Categories with Corresponding Gene Markers
labels2colors
Convert numerical labels to colors.
votingLinearPredictor
Voting linear predictor
corPvalueStudent
Student asymptotic p-value for correlation
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
verboseScatterplot
Scatterplot annotated by regression line and p-value
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
goodGenesMS
Filter genes with too many missing entries across multiple sets
labeledHeatmap
Produce a labeled heatmap plot
redWhiteGreen
Red-white-green color sequence
alignExpr
Align expression data with given vector
labelPoints
Label scatterplot points
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
moduleEigengenes
Calculate module eigengenes.
metaZfunction
Meta-analysis Z statistic
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
preservationNetworkConnectivity
Network preservation calculations
na
Basic Statistical Functions for Handling Missing Values
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
simulateSmallLayer
Simulate small modules
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
Inline display of progress
Inline display of progress
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
exportNetworkToVisANT
Export network data in format readable by VisANT
networkScreeningGS
Network gene screening with an external gene significance measure
addErrorBars
Add error bars to a barplot.
networkConcepts
Calculations of network concepts
plotMEpairs
Pairwise scatterplots of eigengenes
orderMEs
Put close eigenvectors next to each other
plotModuleSignificance
Barplot of module significance
qvalue
Estimate the q-values for a given set of p-values
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
simulateEigengeneNetwork
Simulate eigengene network from a causal model
relativeCorPredictionSuccess
Compare prediction success
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
qvalue.restricted
qvalue convenience wrapper
simulateModule
Simulate a gene co-expression module
spaste
Space-less paste
randIndex
Rand index of two partitions
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
stat.diag.da
Diagonal Discriminant Analysis
clusterCoef
Clustering coefficient calculation
subsetTOM
Topological overlap for a subset of a whole set of genes
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
greenBlackRed
Green-black-red color sequence
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
prepComma
Prepend a comma to a non-empty string
simulateDatExpr5Modules
Simplified simulation of expression data
allowWGCNAThreads
Allow and disable multi-threading for certain WGCNA calculations
addGrid
Add grid lines to an existing plot.
goodGenes
Filter genes with too many missing entries
keepCommonProbes
Keep probes that are shared among given data sets
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
pquantile
Parallel quantile, median, mean
scaleFreePlot
Visual check of scale-free topology
removePrincipalComponents
Remove leading principal components from data
simulateMultiExpr
Simulate multi-set expression data
sizeGrWindow
Opens a graphics window with specified dimensions
adjacency.polyReg
Adjacency matrix based on polynomial regression
bicor
Biweight Midcorrelation
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
mergeCloseModules
Merge close modules in gene expression data
matrixToNetwork
Construct a network from a matrix
correlationPreservation
Preservation of eigengene correlations
setCorrelationPreservation
Summary correlation preservation measure
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
moduleNumber
Fixed-height cut of a dendrogram.
cutreeStaticColor
Constant height tree cut using color labels