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WGCNA (version 1.14)

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

16,020

Version

1.14

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

November 10th, 2011

Functions in WGCNA (1.14)

allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations
SCsLists

Stem Cell-Related Genes with Corresponding Gene Markers
blockwiseConsensusModules

Find consensus modules across several datasets.
goodSamplesMS

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

Calculate module eigengenes.
nPresent

Number of present data entries.
qvalue.restricted

qvalue convenience wrapper
preservationNetworkConnectivity

Network preservation calculations
checkSets

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

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

Constant-height tree cut
BrainLists

Brain-Related Categories with Corresponding Gene Markers
adjacency.polyReg

Adjacency matrix based on polynomial regression
matrixToNetwork

Construct a network from a matrix
consensusOrderMEs

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

Blood Cell Types with Corresponding Gene Markers
networkScreeningGS

Network gene screening with an external gene significance measure
corAndPvalue

Calculation of correlations and associated p-values
modulePreservation

Calculation of module preservation statistics
clusterCoef

Clustering coefficient calculation
bicor

Biweight Midcorrelation
plotCor

Red and Green Color Image of Correlation Matrix
coClustering

Co-clustering measure of cluster preservation between two clusterings
AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
goodSamples

Filter samples with too many missing entries
displayColors

Show colors used to label modules
WGCNA-package

Weighted Gene Co-Expression Network Analysis
plotModuleSignificance

Barplot of module significance
swapTwoBranches

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

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

Consensus dissimilarity of module eigengenes.
conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.
networkConcepts

Calculations of network concepts
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
addGrid

Add grid lines to an existing plot.
moduleColor.getMEprefix

Get the prefix used to label module eigengenes.
goodGenes

Filter genes with too many missing entries
goodGenesMS

Filter genes with too many missing entries across multiple sets
intramodularConnectivity

Calculation of intramodular connectivity
goodSamplesGenes

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

Calculation of fundamental network concepts from an adjacency matrix.
scaleFreePlot

Visual check of scale-free topology
populationMeansInAdmixture

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

Calculate weighted adjacency matrices based on mutual information
plotDendroAndColors

Dendrogram plot with color annotation of objects
nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors
plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples
cutreeStaticColor

Constant height tree cut using color labels
moduleNumber

Fixed-height cut of a dendrogram.
simulateDatExpr5Modules

Simplified simulation of expression data
exportNetworkToCytoscape

Export network to Cytoscape
nearestCentroidPredictor

Nearest centroid predictor
plotNetworkHeatmap

Network heatmap plot
coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model
simulateModule

Simulate a gene co-expression module
consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering
multiSetMEs

Calculate module eigengenes.
accuracyMeasures

Accuracy measures for a 2x2 confusion matrix.
colQuantileC

Fast colunm-wise quantile of a matrix.
chooseOneHubInEachModule

Chooses a single hub gene in each module
conformityDecomposition

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

Proportion of variance explained by eigengenes.
TOMsimilarity

Topological overlap matrix similarity and dissimilarity
pquantile

Parallel quantile, median, mean
addTraitToMEs

Add trait information to multi-set module eigengene structure
pickHardThreshold

Analysis of scale free topology for hard-thresholding.
matchLabels

Relabel module labels to best match the given reference labels
prepComma

Prepend a comma to a non-empty string
alignExpr

Align expression data with given vector
moduleMergeUsingKME

Merge modules and reassign genes using kME.
orderMEs

Put close eigenvectors next to each other
metaAnalysis

Meta-analysis of binary and continuous variables
consensusProjectiveKMeans

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

Label scatterplot points
labeledBarplot

Barplot with text or color labels.
collectGarbage

Iterative garbage collection.
corPredictionSuccess

Qunatification of success of gene screening
coClustering.permutationTest

Permutation test for co-clustering
fixDataStructure

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

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

Calculate overlap of modules
hubGeneSignificance

Hubgene significance
redWhiteGreen

Red-white-green color sequence
labels2colors

Convert numerical labels to colors.
mergeCloseModules

Merge close modules in gene expression data
kMEcomparisonScatterplot

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

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

Fisher's asymptotic p-value for correlation
relativeCorPredictionSuccess

Compare prediction success
TOMsimilarityFromExpr

Topological overlap matrix
GOenrichmentAnalysis

Calculation of GO enrichment (experimental)
sigmoidAdjacencyFunction

Sigmoid-type adacency function.
rankPvalue

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

Generalized Topological Overlap Measure
corPvalueStudent

Student asymptotic p-value for correlation
pickSoftThreshold

Analysis of scale free topology for soft-thresholding
adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression
chooseTopHubInEachModule

Chooses the top hub gene in each module
removePrincipalComponents

Remove leading principal components from data
proportionsInAdmixture

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

Signed eigengene-based connectivity
plotMEpairs

Pairwise scatterplots of eigengenes
TOMplot

Graphical representation of the Topological Overlap Matrix
simulateEigengeneNetwork

Simulate eigengene network from a causal model
stdErr

Standard error of the mean of a given vector.
automaticNetworkScreening

One-step automatic network gene screening
signumAdjacencyFunction

Hard-thresholding adjacency function
greenBlackRed

Green-black-red color sequence
metaZfunction

Meta-analysis Z statistic
sizeGrWindow

Opens a graphics window with specified dimensions
Inline display of progress

Inline display of progress
bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values
simulateMultiExpr

Simulate multi-set expression data
rgcolors.func

Red and Green Color Specification
plotMat

Red and Green Color Image of Data Matrix
stat.diag.da

Diagonal Discriminant Analysis
checkAdjMat

Check adjacency matrix
stat.bwss

Between and Within Group Sum of Squares Calculation
numbers2colors

Color representation for a numeric variable
adjacency

Calculate network adjacency
projectiveKMeans

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

Colors this library uses for labeling modules.
simulateSmallLayer

Simulate small modules
qvalue

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

Rand index of two partitions
removeGreyME

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

Automatic network construction and module detection
correlationPreservation

Preservation of eigengene correlations
labeledHeatmap

Produce a labeled heatmap plot
recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data
recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data
collapseRowsUsingKME

Selects one representative row per group based on kME
simulateDatExpr

Simulation of expression data
spaste

Space-less paste
cor

Fast calculations of Pearson correlation.
exportNetworkToVisANT

Export network data in format readable by VisANT
networkScreening

Identification of genes related to a trait
softConnectivity

Calculates connectivity of a weighted network.
plotEigengeneNetworks

Eigengene network plot
standardScreeningNumericTrait

Standard screening for numeric traits
standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable
vectorizeMatrix

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

Scatterplot annotated by regression line and p-value
unsignedAdjacency

Calculation of unsigned adjacency
verboseBarplot

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

Boxplot annotated by a Kruskal-Wallis p-value
votingLinearPredictor

Voting linear predictor
setCorrelationPreservation

Summary correlation preservation measure
userListEnrichment

Measure enrichment between inputted and user-defined lists
verboseIplot

Scatterplot with density
subsetTOM

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

Threshold for module merging
greenWhiteRed

Green-white-red color sequence
scaleFreeFitIndex

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

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

Add error bars to a barplot.
collapseRows

Select one representative row per group
keepCommonProbes

Keep probes that are shared among given data sets
na

Basic Statistical Functions for Handling Missing Values
normalizeLabels

Transform numerical labels into normal order.
orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.
plotColorUnderTree

Plot color rows under a dendrogram
overlapTableUsingKME

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

Standard screening for binatry traits