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WGCNA (version 1.41-1)
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
1.41-1
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
June 14th, 2014
Functions in WGCNA (1.41-1)
Search functions
BrainLists
Brain-Related Categories with Corresponding Gene Markers
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
collapseRows
Select one representative row per group
blockwiseConsensusModules
Find consensus modules across several datasets.
preservationNetworkConnectivity
Network preservation calculations
BloodLists
Blood Cell Types with Corresponding Gene Markers
TOMsimilarityFromExpr
Topological overlap matrix
labeledBarplot
Barplot with text or color labels.
networkScreeningGS
Network gene screening with an external gene significance measure
scaleFreePlot
Visual check of scale-free topology
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
corAndPvalue
Calculation of correlations and associated p-values
stratifiedBarplot
Bar plots of data across two splitting parameters
shortenStrings
Shorten given character strings by truncating at a suitable separator.
mtd.apply
Apply a function to each set in a multiData structure.
signedKME
Signed eigengene-based connectivity
userListEnrichment
Measure enrichment between inputted and user-defined lists
networkScreening
Identification of genes related to a trait
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
spaste
Space-less paste
simulateEigengeneNetwork
Simulate eigengene network from a causal model
addErrorBars
Add error bars to a barplot.
greenWhiteRed
Green-white-red color sequence
alignExpr
Align expression data with given vector
vectorTOM
Topological overlap for a subset of the whole set of genes
cor
Fast calculations of Pearson correlation.
blockwiseIndividualTOMs
Calculation of block-wise topological overlaps
adjacency.polyReg
Adjacency matrix based on polynomial regression
lowerTri2matrix
Reconstruct a symmetric matrix from a distance (lower-triangular) representation
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
labels2colors
Convert numerical labels to colors.
mtd.subset
Subset rows and columns in a multiData structure
multiUnion
Union and intersection of multiple sets
coClustering.permutationTest
Permutation test for co-clustering
labelPoints
Label scatterplot points
moduleEigengenes
Calculate module eigengenes.
nPresent
Number of present data entries.
normalizeLabels
Transform numerical labels into normal order.
plotDendroAndColors
Dendrogram plot with color annotation of objects
propVarExplained
Proportion of variance explained by eigengenes.
mtd.rbindSelf
Turn a multiData structure into a single matrix or data frame.
plotModuleSignificance
Barplot of module significance
returnGeneSetsAsList
Return pre-defined gene lists in several biomedical categories.
simulateModule
Simulate a gene co-expression module
unsignedAdjacency
Calculation of unsigned adjacency
stat.bwss
Between and Within Group Sum of Squares Calculation
votingLinearPredictor
Voting linear predictor
softConnectivity
Calculates connectivity of a weighted network.
simulateSmallLayer
Simulate small modules
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
WGCNA-package
Weighted Gene Co-Expression Network Analysis
SCsLists
Stem Cell-Related Genes with Corresponding Gene Markers
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
BrainRegionMarkers
Gene Markers for Regions of the Human Brain
addTraitToMEs
Add trait information to multi-set module eigengene structure
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
blockSize
Attempt to calculate an appropriate block size to maximize efficiency of block-wise calcualtions.
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix or for vectors of predicted and observed values.
checkAdjMat
Check adjacency matrix
multiData.eigengeneSignificance
Eigengene significance across multiple sets
exportNetworkToVisANT
Export network data in format readable by VisANT
overlapTable
Calculate overlap of modules
addGrid
Add grid lines to an existing plot.
na
Basic Statistical Functions for Handling Missing Values
GTOMdist
Generalized Topological Overlap Measure
cutreeStatic
Constant-height tree cut
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
plotColorUnderTree
Plot color rows in a given order, for example under a dendrogram
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
corPvalueFisher
Fisher's asymptotic p-value for correlation
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
correlationPreservation
Preservation of eigengene correlations
TrueTrait
Estimate the true trait underlying a list of surrogate markers.
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
exportNetworkToCytoscape
Export network to Cytoscape
TOMplot
Graphical representation of the Topological Overlap Matrix
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
modulePreservation
Calculation of module preservation statistics
nSets
Number of sets in a multi-set variable
corPredictionSuccess
Qunatification of success of gene screening
qvalue
Estimate the q-values for a given set of p-values
greenBlackRed
Green-black-red color sequence
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
simulateDatExpr
Simulation of expression data
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
metaAnalysis
Meta-analysis of binary and continuous variables
allowWGCNAThreads
Allow and disable multi-threading for certain WGCNA calculations
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
Inline display of progress
Inline display of progress
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
plotNetworkHeatmap
Network heatmap plot
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
plotEigengeneNetworks
Eigengene network plot
mergeCloseModules
Merge close modules in gene expression data
formatLabels
Break long character strings into multiple lines
chooseTopHubInEachModule
Chooses the top hub gene in each module
projectiveKMeans
Projective K-means (pre-)clustering of expression data
list2multiData
Convert a list to a multiData structure and vice-versa.
verboseIplot
Scatterplot with density
plotCor
Red and Green Color Image of Correlation Matrix
branchSplit.dissim
Branch split based on dissimilarity.
mtd.simplify
If possible, simplify a multiData structure to a 3-dimensional array.
randIndex
Rand index of two partitions
collectGarbage
Iterative garbage collection.
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
simulateDatExpr5Modules
Simplified simulation of expression data
corPvalueStudent
Student asymptotic p-value for correlation
goodGenesMS
Filter genes with too many missing entries across multiple sets
displayColors
Show colors used to label modules
ImmunePathwayLists
Immune Pathways with Corresponding Gene Markers
networkConcepts
Calculations of network concepts
sizeGrWindow
Opens a graphics window with specified dimensions
adjacency
Calculate network adjacency
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
labeledHeatmap.multiPage
Labeled heatmap divided into several separate plots.
standardColors
Colors this library uses for labeling modules.
blueWhiteRed
Blue-white-red color sequence
branchEigengeneDissim
Branch dissimilarity based on eigennodes (eigengenes).
qvalue.restricted
qvalue convenience wrapper
fixDataStructure
Put single-set data into a form useful for multiset calculations.
colQuantileC
Fast colunm-wise quantile of a matrix.
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
rgcolors.func
Red and Green Color Specification
subsetTOM
Topological overlap for a subset of a whole set of genes
chooseOneHubInEachModule
Chooses a single hub gene in each module
setCorrelationPreservation
Summary correlation preservation measure
goodSamples
Filter samples with too many missing entries
keepCommonProbes
Keep probes that are shared among given data sets
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
matchLabels
Relabel module labels to best match the given reference labels
standardScreeningBinaryTrait
Standard screening for binatry traits
consensusKME
Calculate consensus kME (eigengene-based connectivities) across multiple data sets.
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
orderMEs
Put close eigenvectors next to each other
blockwiseModules
Automatic network construction and module detection
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
hubGeneSignificance
Hubgene significance
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
branchSplit
Branch split.
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
relativeCorPredictionSuccess
Compare prediction success
multiData
Create a multiData structure.
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
signumAdjacencyFunction
Hard-thresholding adjacency function
numbers2colors
Color representation for a numeric variable
simulateMultiExpr
Simulate multi-set expression data
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
stdErr
Standard error of the mean of a given vector.
prepComma
Prepend a comma to a non-empty string
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
clusterCoef
Clustering coefficient calculation
removePrincipalComponents
Remove leading principal components from data
intramodularConnectivity
Calculation of intramodular connectivity
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
automaticNetworkScreening
One-step automatic network gene screening
standardScreeningNumericTrait
Standard screening for numeric traits
dynamicMergeCut
Threshold for module merging
mtd.setColnames
Get and set column names in a multiData structure.
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
plotMat
Red and Green Color Image of Data Matrix
goodGenes
Filter genes with too many missing entries
multiSetMEs
Calculate module eigengenes.
allocateJobs
Divide tasks among workers
stat.diag.da
Diagonal Discriminant Analysis
verboseScatterplot
Scatterplot annotated by regression line and p-value
moduleNumber
Fixed-height cut of a dendrogram.
bicor
Biweight Midcorrelation
labeledHeatmap
Produce a labeled heatmap plot
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
checkSets
Check structure and retrieve sizes of a group of datasets.
coClustering
Co-clustering measure of cluster preservation between two clusterings
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
matrixToNetwork
Construct a network from a matrix
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
transposeBigData
Transpose a big matrix or data frame
metaZfunction
Meta-analysis Z statistic
prependZeros
Pad numbers with leading zeros to specified total width
plotMEpairs
Pairwise scatterplots of eigengenes
mtd.setAttr
Set attributes on each component of a multiData structure
PWLists
Pathways with Corresponding Gene Markers - Compiled by Mike Palazzolo and Jim Wang from CHDI
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
cutreeStaticColor
Constant height tree cut using color labels
moduleMergeUsingKME
Merge modules and reassign genes using kME.
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
collapseRowsUsingKME
Selects one representative row per group based on kME
mtd.mapply
Apply a function to elements of given multiData structures.
isMultiData
Determine whether the supplied object is a valid multiData structure
nearestCentroidPredictor
Nearest centroid predictor
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
pquantile
Parallel quantile, median, mean
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
redWhiteGreen
Red-white-green color sequence