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WGCNA (version 1.11-3)

Weighted Gene Co-Expression Network Analysis

Description

Functions necessary to perform Weighted Gene Co-Expression Network Analysis

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Version

Install

install.packages('WGCNA')

Monthly Downloads

13,041

Version

1.11-3

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

July 7th, 2011

Functions in WGCNA (1.11-3)

correlationPreservation

Preservation of eigengene correlations
cutreeStatic

Constant-height tree cut
automaticNetworkScreening

One-step automatic network gene screening
matrixToNetwork

Construct a network from a matrix
clusterCoef

Clustering coefficient calculation
adjacency

Calculate network adjacency
preservationNetworkConnectivity

Network preservation calculations
mergeCloseModules

Merge close modules in gene expression data
checkAdjMat

Check adjacency matrix
TOMsimilarity

Topological overlap matrix similarity and dissimilarity
swapTwoBranches

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

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

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

Align expression data with given vector
plotNetworkHeatmap

Network heatmap plot
BloodLists

Blood Cell Types with Corresponding Gene Markers
verboseBarplot

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

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

Calculate weighted adjacency matrices based on mutual information
addErrorBars

Add error bars to a barplot.
GOenrichmentAnalysis

Calculation of GO enrichment (experimental)
conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.
TOMplot

Graphical representation of the Topological Overlap Matrix
consensusProjectiveKMeans

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

Show colors used to label modules
addGrid

Add grid lines to an existing plot.
accuracyMeasures

Accuracy measures for a 2x2 confusion matrix.
cutreeStaticColor

Constant height tree cut using color labels
BrainLists

Brain-Related Categories with Corresponding Gene Markers
pquantile

Parallel quantile, median, mean
adjacency.polyReg

Adjacency matrix based on polynomial regression
consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering
collapseRows

Select one representative row per group
projectiveKMeans

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

Annotated clustering dendrogram of microarray samples
coClustering

Co-clustering measure of cluster preservation between two clusterings
simulateDatExpr5Modules

Simplified simulation of expression data
propVarExplained

Proportion of variance explained by eigengenes.
corPvalueFisher

Fisher's asymptotic p-value for correlation
exportNetworkToVisANT

Export network data in format readable by VisANT
labels2colors

Convert numerical labels to colors.
dynamicMergeCut

Threshold for module merging
overlapTableUsingKME

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

Generalized Topological Overlap Measure
greenWhiteRed

Green-white-red color sequence
vectorTOM

Topological overlap for a subset of the whole set of genes
coClustering.permutationTest

Permutation test for co-clustering
chooseTopHubInEachModule

Chooses the top hub gene in each module
nPresent

Number of present data entries.
rankPvalue

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

Calculate network adjacency based on natural cubic spline regression
goodSamples

Filter samples with too many missing entries
standardScreeningNumericTrait

Standard screening for numeric traits
chooseOneHubInEachModule

Chooses a single hub gene in each module
addTraitToMEs

Add trait information to multi-set module eigengene structure
colQuantileC

Fast colunm-wise quantile of a matrix.
corAndPvalue

Calculation of correlations and associated p-values
labeledHeatmap

Produce a labeled heatmap plot
consensusOrderMEs

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

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

Fixed-height cut of a dendrogram.
moduleEigengenes

Calculate module eigengenes.
collectGarbage

Iterative garbage collection.
modulePreservation

Calculation of module preservation statistics
consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.
metaZfunction

Meta-analysis Z statistic
orderMEs

Put close eigenvectors next to each other
multiSetMEs

Calculate module eigengenes.
moduleColor.getMEprefix

Get the prefix used to label module eigengenes.
userListEnrichment

Measure enrichment between inputted and user-defined lists
goodSamplesGenes

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

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

Scatterplot annotated by regression line and p-value
removeGreyME

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

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

Basic Statistical Functions for Handling Missing Values
conformityDecomposition

Conformity and module based decomposition of a network adjacency matrix.
plot.mat

Red and Green Color Image of Data Matrix
nearestCentroidPredictor

Nearest centroid predictor
plotMEpairs

Pairwise scatterplots of eigengenes
sizeGrWindow

Opens a graphics window with specified dimensions
TOMsimilarityFromExpr

Topological overlap matrix
addGuideLines

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

Simulate small modules
redWhiteGreen

Red-white-green color sequence
bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values
checkSets

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

Rand index of two partitions
blockwiseModules

Automatic network construction and module detection
goodGenesMS

Filter genes with too many missing entries across multiple sets
kMEcomparisonScatterplot

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

Analysis of scale free topology for soft-thresholding
labeledBarplot

Barplot with text or color labels.
plotEigengeneNetworks

Eigengene network plot
labelPoints

Label scatterplot points
signumAdjacencyFunction

Hard-thresholding adjacency function
proportionsInAdmixture

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

Calculation of intramodular connectivity
networkScreening

Identification of genes related to a trait
AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
normalizeLabels

Transform numerical labels into normal order.
nearestNeighborConnectivityMS

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

Biweight Midcorrelation
stat.bwss

Between and Within Group Sum of Squares Calculation
collapseRowsUsingKME

Selects one representative row per group based on kME
numbers2colors

Color representation for a numeric variable
nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors
standardColors

Colors this library uses for labeling modules.
spaste

Space-less paste
networkScreeningGS

Network gene screening with an external gene significance measure
simulateEigengeneNetwork

Simulate eigengene network from a causal model
qvalue

Estimate the q-values for a given set of p-values
simulateModule

Simulate a gene co-expression module
matchLabels

Relabel module labels to best match the given reference labels
recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data
orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.
corPvalueStudent

Student asymptotic p-value for correlation
setCorrelationPreservation

Summary correlation preservation measure
signedKME

Signed eigengene-based connectivity
softConnectivity

Calculates connectivity of a weighted network.
stat.diag.da

Diagonal Discriminant Analysis
verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value
hubGeneSignificance

Hubgene significance
cor

Fast calculations of Pearson correlation.
networkConcepts

Calculations of network concepts
plotModuleSignificance

Barplot of module significance
stdErr

Standard error of the mean of a given vector.
standardScreeningBinaryTrait

Standard screening for binatry traits
Inline display of progress

Inline display of progress
goodGenes

Filter genes with too many missing entries
plotDendroAndColors

Dendrogram plot with color annotation of objects
vectorizeMatrix

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

Voting linear predictor
relativeCorPredictionSuccess

Compare prediction success
unsignedAdjacency

Calculation of unsigned adjacency
keepCommonProbes

Keep probes that are shared among given data sets
removePrincipalComponents

Remove leading principal components from data
greenBlackRed

Green-black-red color sequence
scaleFreePlot

Visual check of scale-free topology
pickHardThreshold

Analysis of scale free topology for hard-thresholding.
standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable
overlapTable

Calculate overlap of modules
fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.
plot.cor

Red and Green Color Image of Correlation Matrix
moduleMergeUsingKME

Merge modules and reassign genes using kME.
plotColorUnderTree

Plot color rows under a dendrogram
recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data
simulateDatExpr

Simulation of expression data
simulateMultiExpr

Simulate multi-set expression data
corPredictionSuccess

Qunatification of success of gene screening
coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model
exportNetworkToCytoscape

Export network to Cytoscape
prepComma

Prepend a comma to a non-empty string
sigmoidAdjacencyFunction

Sigmoid-type adacency function.
rgcolors.func

Red and Green Color Specification
subsetTOM

Topological overlap for a subset of a whole set of genes
WGCNA-package

Weighted Gene Co-Expression Network Analysis
blockwiseConsensusModules

Find consensus modules across several datasets.
stratifiedBarplot

Bar plots of data across two splitting parameters