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 1.34)
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
1.34
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
October 10th, 2013
Functions in WGCNA (1.34)
Search functions
cutreeStatic
Constant-height tree cut
PWLists
Pathways with Corresponding Gene Markers - Compiled by Mike Palazzolo and Jim Wang from CHDI
labels2colors
Convert numerical labels to colors.
blockwiseIndividualTOMs
Calculation of block-wise topological overlaps
colQuantileC
Fast colunm-wise quantile of a matrix.
allowWGCNAThreads
Allow and disable multi-threading for certain WGCNA calculations
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
numbers2colors
Color representation for a numeric variable
blueWhiteRed
Blue-white-red color sequence
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
pquantile
Parallel quantile, median, mean
SCsLists
Stem Cell-Related Genes with Corresponding Gene Markers
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
alignExpr
Align expression data with given vector
adjacency
Calculate network adjacency
returnGeneSetsAsList
Return pre-defined gene lists in several biomedical categories.
overlapTable
Calculate overlap of modules
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
BrainLists
Brain-Related Categories with Corresponding Gene Markers
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
softConnectivity
Calculates connectivity of a weighted network.
displayColors
Show colors used to label modules
multiSetMEs
Calculate module eigengenes.
mtd.subset
Subset rows and columns in a multiData structure
moduleMergeUsingKME
Merge modules and reassign genes using kME.
orderMEs
Put close eigenvectors next to each other
addTraitToMEs
Add trait information to multi-set module eigengene structure
plotColorUnderTree
Plot color rows in a given order, for example under a dendrogram
blockwiseModules
Automatic network construction and module detection
stat.bwss
Between and Within Group Sum of Squares Calculation
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
branchSplit.dissim
Branch split based on dissimilarity.
networkConcepts
Calculations of network concepts
vectorTOM
Topological overlap for a subset of the whole set of genes
plotMat
Red and Green Color Image of Data Matrix
propVarExplained
Proportion of variance explained by eigengenes.
consensusKME
Calculate consensus kME (eigengene-based connectivities) across multiple data sets.
plotMEpairs
Pairwise scatterplots of eigengenes
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
spaste
Space-less paste
redWhiteGreen
Red-white-green color sequence
stdErr
Standard error of the mean of a given vector.
modulePreservation
Calculation of module preservation statistics
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
cor
Fast calculations of Pearson correlation.
simulateEigengeneNetwork
Simulate eigengene network from a causal model
simulateSmallLayer
Simulate small modules
subsetTOM
Topological overlap for a subset of a whole set of genes
goodSamples
Filter samples with too many missing entries
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
qvalue.restricted
qvalue convenience wrapper
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
labeledHeatmap
Produce a labeled heatmap plot
corAndPvalue
Calculation of correlations and associated p-values
projectiveKMeans
Projective K-means (pre-)clustering of expression data
checkSets
Check structure and retrieve sizes of a group of datasets.
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
BrainRegionMarkers
Gene Markers for Regions of the Human Brain
collapseRowsUsingKME
Selects one representative row per group based on kME
dynamicMergeCut
Threshold for module merging
na
Basic Statistical Functions for Handling Missing Values
exportNetworkToVisANT
Export network data in format readable by VisANT
keepCommonProbes
Keep probes that are shared among given data sets
addGrid
Add grid lines to an existing plot.
mtd.mapply
Apply a function to elements of given multiData structures.
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
intramodularConnectivity
Calculation of intramodular connectivity
isMultiData
Determine whether the supplied object is a valid multiData structure
TOMplot
Graphical representation of the Topological Overlap Matrix
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
branchEigengeneDissim
Branch dissimilarity based on eigennodes (eigengenes).
chooseTopHubInEachModule
Chooses the top hub gene in each module
blockwiseConsensusModules
Find consensus modules across several datasets.
mergeCloseModules
Merge close modules in gene expression data
rgcolors.func
Red and Green Color Specification
verboseScatterplot
Scatterplot annotated by regression line and p-value
TOMsimilarityFromExpr
Topological overlap matrix
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
moduleNumber
Fixed-height cut of a dendrogram.
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
ImmunePathwayLists
Immune Pathways with Corresponding Gene Markers
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
checkAdjMat
Check adjacency matrix
transposeBigData
Transpose a big matrix or data frame
WGCNA-package
Weighted Gene Co-Expression Network Analysis
corPredictionSuccess
Qunatification of success of gene screening
list2multiData
Convert a list to a multiData structure and vice-versa.
sizeGrWindow
Opens a graphics window with specified dimensions
cutreeStaticColor
Constant height tree cut using color labels
collectGarbage
Iterative garbage collection.
networkScreening
Identification of genes related to a trait
metaZfunction
Meta-analysis Z statistic
goodGenes
Filter genes with too many missing entries
preservationNetworkConnectivity
Network preservation calculations
standardColors
Colors this library uses for labeling modules.
labelPoints
Label scatterplot points
simulateMultiExpr
Simulate multi-set expression data
adjacency.polyReg
Adjacency matrix based on polynomial regression
TrueTrait
Estimate the true trait underlying a list of surrogate markers.
corPvalueFisher
Fisher's asymptotic p-value for correlation
coClustering.permutationTest
Permutation test for co-clustering
clusterCoef
Clustering coefficient calculation
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
hubGeneSignificance
Hubgene significance
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
lowerTri2matrix
Reconstruct a symmetric matrix from a distance (lower-triangular) representation
goodGenesMS
Filter genes with too many missing entries across multiple sets
matchLabels
Relabel module labels to best match the given reference labels
scaleFreePlot
Visual check of scale-free topology
stratifiedBarplot
Bar plots of data across two splitting parameters
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
verboseIplot
Scatterplot with density
votingLinearPredictor
Voting linear predictor
plotNetworkHeatmap
Network heatmap plot
nearestCentroidPredictor
Nearest centroid predictor
metaAnalysis
Meta-analysis of binary and continuous variables
networkScreeningGS
Network gene screening with an external gene significance measure
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
signumAdjacencyFunction
Hard-thresholding adjacency function
fixDataStructure
Put single-set data into a form useful for multiset calculations.
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
matrixToNetwork
Construct a network from a matrix
qvalue
Estimate the q-values for a given set of p-values
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
Inline display of progress
Inline display of progress
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
mtd.simplify
If possible, simplify a multiData structure to a 3-dimensional array.
nSets
Number of sets in a multi-set variable
signedKME
Signed eigengene-based connectivity
standardScreeningNumericTrait
Standard screening for numeric traits
addErrorBars
Add error bars to a barplot.
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
allocateJobs
Divide tasks among workers
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix or for vectors of predicted and observed values.
coClustering
Co-clustering measure of cluster preservation between two clusterings
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
userListEnrichment
Measure enrichment between inputted and user-defined lists
mtd.apply
Apply a function to each set in a multiData structure.
blockSize
Attempt to calculate an appropriate block size to maximize efficiency of block-wise calcualtions.
collapseRows
Select one representative row per group
multiData.eigengeneSignificance
Eigengene significance across multiple sets
plotModuleSignificance
Barplot of module significance
removePrincipalComponents
Remove leading principal components from data
BloodLists
Blood Cell Types with Corresponding Gene Markers
mtd.setColnames
Get and set column names in a multiData structure.
plotEigengeneNetworks
Eigengene network plot
greenWhiteRed
Green-white-red color sequence
plotCor
Red and Green Color Image of Correlation Matrix
nPresent
Number of present data entries.
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
plotDendroAndColors
Dendrogram plot with color annotation of objects
setCorrelationPreservation
Summary correlation preservation measure
stat.diag.da
Diagonal Discriminant Analysis
simulateDatExpr5Modules
Simplified simulation of expression data
relativeCorPredictionSuccess
Compare prediction success
chooseOneHubInEachModule
Chooses a single hub gene in each module
automaticNetworkScreening
One-step automatic network gene screening
corPvalueStudent
Student asymptotic p-value for correlation
mtd.setAttr
Set attributes on each component of a multiData structure
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
randIndex
Rand index of two partitions
standardScreeningBinaryTrait
Standard screening for binatry traits
simulateDatExpr
Simulation of expression data
unsignedAdjacency
Calculation of unsigned adjacency
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
GTOMdist
Generalized Topological Overlap Measure
bicor
Biweight Midcorrelation
moduleEigengenes
Calculate module eigengenes.
greenBlackRed
Green-black-red color sequence
normalizeLabels
Transform numerical labels into normal order.
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
branchSplit
Branch split.
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
correlationPreservation
Preservation of eigengene correlations
exportNetworkToCytoscape
Export network to Cytoscape
labeledBarplot
Barplot with text or color labels.
mtd.rbindSelf
Turn a multiData structure into a single matrix or data frame.
prepComma
Prepend a comma to a non-empty string
simulateModule
Simulate a gene co-expression module