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WGCNA (version 1.26)

Weighted Correlation Network Analysis

Description

Functions necessary to perform Weighted Correlation Network Analysis.

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Version

Install

install.packages('WGCNA')

Monthly Downloads

16,020

Version

1.26

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

March 7th, 2013

Functions in WGCNA (1.26)

TOMplot

Graphical representation of the Topological Overlap Matrix
metaZfunction

Meta-analysis Z statistic
SCsLists

Stem Cell-Related Genes with Corresponding Gene Markers
consensusKME

Calculate consensus kME (eigengene-based connectivities) across multiple data sets.
blockwiseConsensusModules

Find consensus modules across several datasets.
TOMsimilarityFromExpr

Topological overlap matrix
displayColors

Show colors used to label modules
collectGarbage

Iterative garbage collection.
goodSamples

Filter samples with too many missing entries
corPredictionSuccess

Qunatification of success of gene screening
fixDataStructure

Put single-set data into a form useful for multiset calculations.
removeGreyME

Removes the grey eigengene from a given collection of eigengenes.
signumAdjacencyFunction

Hard-thresholding adjacency function
rankPvalue

Estimate the p-value for ranking consistently high (or low) on multiple lists
labelPoints

Label scatterplot points
scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.
cor

Fast calculations of Pearson correlation.
WGCNA-package

Weighted Gene Co-Expression Network Analysis
setCorrelationPreservation

Summary correlation preservation measure
corPvalueFisher

Fisher's asymptotic p-value for correlation
pquantile

Parallel quantile, median, mean
goodGenesMS

Filter genes with too many missing entries across multiple sets
orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.
coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model
matchLabels

Relabel module labels to best match the given reference labels
standardScreeningNumericTrait

Standard screening for numeric traits
corAndPvalue

Calculation of correlations and associated p-values
blockwiseIndividualTOMs

Calculation of block-wise topological overlaps
greenBlackRed

Green-black-red color sequence
kMEcomparisonScatterplot

Function to plot kME values between two comparable data sets.
dynamicMergeCut

Threshold for module merging
addGrid

Add grid lines to an existing plot.
AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance
blockwiseModules

Automatic network construction and module detection
accuracyMeasures

Accuracy measures for a 2x2 confusion matrix or for vectors of predicted and observed values.
bicor

Biweight Midcorrelation
adjacency

Calculate network adjacency
intramodularConnectivity

Calculation of intramodular connectivity
removePrincipalComponents

Remove leading principal components from data
verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value
metaAnalysis

Meta-analysis of binary and continuous variables
chooseTopHubInEachModule

Chooses the top hub gene in each module
nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors
modulePreservation

Calculation of module preservation statistics
coClustering.permutationTest

Permutation test for co-clustering
adjacency.polyReg

Adjacency matrix based on polynomial regression
colQuantileC

Fast colunm-wise quantile of a matrix.
moduleEigengenes

Calculate module eigengenes.
collapseRowsUsingKME

Selects one representative row per group based on kME
mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information
populationMeansInAdmixture

Estimate the population-specific mean values in an admixed population.
pickHardThreshold

Analysis of scale free topology for hard-thresholding.
multiData.eigengeneSignificance

Eigengene significance across multiple sets
networkScreeningGS

Network gene screening with an external gene significance measure
greenWhiteRed

Green-white-red color sequence
qvalue.restricted

qvalue convenience wrapper
moduleColor.getMEprefix

Get the prefix used to label module eigengenes.
clusterCoef

Clustering coefficient calculation
simulateSmallLayer

Simulate small modules
stat.bwss

Between and Within Group Sum of Squares Calculation
checkSets

Check structure and retrieve sizes of a group of datasets.
networkScreening

Identification of genes related to a trait
goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries
normalizeLabels

Transform numerical labels into normal order.
sizeGrWindow

Opens a graphics window with specified dimensions
simulateModule

Simulate a gene co-expression module
hubGeneSignificance

Hubgene significance
plotDendroAndColors

Dendrogram plot with color annotation of objects
plotEigengeneNetworks

Eigengene network plot
swapTwoBranches

Select, swap, or reflect branches in a dendrogram.
consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.
moduleNumber

Fixed-height cut of a dendrogram.
goodSamplesMS

Filter samples with too many missing entries across multiple data sets
nSets

Number of sets in a multi-set variable
labels2colors

Convert numerical labels to colors.
prepComma

Prepend a comma to a non-empty string
softConnectivity

Calculates connectivity of a weighted network.
recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data
orderMEs

Put close eigenvectors next to each other
redWhiteGreen

Red-white-green color sequence
stat.diag.da

Diagonal Discriminant Analysis
addGuideLines

Add vertical ``guide lines'' to a dendrogram plot
nearestNeighborConnectivityMS

Connectivity to a constant number of nearest neighbors across multiple data sets
plotCor

Red and Green Color Image of Correlation Matrix
plotMEpairs

Pairwise scatterplots of eigengenes
propVarExplained

Proportion of variance explained by eigengenes.
preservationNetworkConnectivity

Network preservation calculations
lowerTri2matrix

Reconstruct a symmetric matrix from a distance (lower-triangular) representation
GOenrichmentAnalysis

Calculation of GO enrichment (experimental)
verboseIplot

Scatterplot with density
blockSize

Attempt to calculate an appropriate block size to maximize efficiency of block-wise calcualtions.
simulateDatExpr5Modules

Simplified simulation of expression data
BrainRegionMarkers

Gene Markers for Regions of the Human Brain
cutreeStatic

Constant-height tree cut
overlapTable

Calculate overlap of modules
plotNetworkHeatmap

Network heatmap plot
vectorizeMatrix

Turn a matrix into a vector of non-redundant components
goodSamplesGenesMS

Iterative filtering of samples and genes with too many missing entries across multiple data sets
labeledHeatmap

Produce a labeled heatmap plot
randomGLMpredictor

Random generalized linear model predictor
GTOMdist

Generalized Topological Overlap Measure
verboseScatterplot

Scatterplot annotated by regression line and p-value
relativeCorPredictionSuccess

Compare prediction success
goodGenes

Filter genes with too many missing entries
plotMat

Red and Green Color Image of Data Matrix
conformityDecomposition

Conformity and module based decomposition of a network adjacency matrix.
transposeBigData

Transpose a big matrix or data frame
rgcolors.func

Red and Green Color Specification
votingLinearPredictor

Voting linear predictor
na

Basic Statistical Functions for Handling Missing Values
randIndex

Rand index of two partitions
nPresent

Number of present data entries.
recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data
stratifiedBarplot

Bar plots of data across two splitting parameters
plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples
simulateEigengeneNetwork

Simulate eigengene network from a causal model
BrainLists

Brain-Related Categories with Corresponding Gene Markers
userListEnrichment

Measure enrichment between inputted and user-defined lists
addErrorBars

Add error bars to a barplot.
spaste

Space-less paste
allocateJobs

Divide tasks among workers
coClustering

Co-clustering measure of cluster preservation between two clusterings
corPvalueStudent

Student asymptotic p-value for correlation
ImmunePathwayLists

Immune Pathways with Corresponding Gene Markers
alignExpr

Align expression data with given vector
automaticNetworkScreening

One-step automatic network gene screening
matrixToNetwork

Construct a network from a matrix
TrueTrait

Estimate the true trait underlying a list of surrogate markers.
adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression
bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values
mergeCloseModules

Merge close modules in gene expression data
chooseOneHubInEachModule

Chooses a single hub gene in each module
TOMsimilarity

Topological overlap matrix similarity and dissimilarity
fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.
checkAdjMat

Check adjacency matrix
nearestCentroidPredictor

Nearest centroid predictor
stdErr

Standard error of the mean of a given vector.
proportionsInAdmixture

Estimate the proportion of pure populations in an admixed population based on marker expression values.
allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations
BloodLists

Blood Cell Types with Corresponding Gene Markers
moduleMergeUsingKME

Merge modules and reassign genes using kME.
numbers2colors

Color representation for a numeric variable
networkConcepts

Calculations of network concepts
scaleFreePlot

Visual check of scale-free topology
signedKME

Signed eigengene-based connectivity
sigmoidAdjacencyFunction

Sigmoid-type adacency function.
consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering
simulateDatExpr

Simulation of expression data
standardColors

Colors this library uses for labeling modules.
correlationPreservation

Preservation of eigengene correlations
cutreeStaticColor

Constant height tree cut using color labels
unsignedAdjacency

Calculation of unsigned adjacency
verboseBarplot

Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.
multiSetMEs

Calculate module eigengenes.
standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable
projectiveKMeans

Projective K-means (pre-)clustering of expression data
subsetTOM

Topological overlap for a subset of a whole set of genes
addTraitToMEs

Add trait information to multi-set module eigengene structure
labeledBarplot

Barplot with text or color labels.
overlapTableUsingKME

Determines significant overlap between modules in two networks based on kME tables.
plotColorUnderTree

Plot color rows under a dendrogram
qvalue

Estimate the q-values for a given set of p-values
Inline display of progress

Inline display of progress
simulateMultiExpr

Simulate multi-set expression data
returnGeneSetsAsList

Return pre-defined gene lists in several biomedical categories.
blueWhiteRed

Blue-white-red color sequence
collapseRows

Select one representative row per group
consensusProjectiveKMeans

Consensus projective K-means (pre-)clustering of expression data
consensusOrderMEs

Put close eigenvectors next to each other in several sets.
exportNetworkToVisANT

Export network data in format readable by VisANT
keepCommonProbes

Keep probes that are shared among given data sets
pickSoftThreshold

Analysis of scale free topology for soft-thresholding
plotModuleSignificance

Barplot of module significance
standardScreeningBinaryTrait

Standard screening for binatry traits
vectorTOM

Topological overlap for a subset of the whole set of genes
exportNetworkToCytoscape

Export network to Cytoscape