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WGCNA (version 1.11-1)

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

11,673

Version

1.11-1

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

June 1st, 2011

Functions in WGCNA (1.11-1)

addGuideLines

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

Blood Cell Types with Corresponding Gene Markers
BrainLists

Brain-Related Categories with Corresponding Gene Markers
addErrorBars

Add error bars to a barplot.
cutreeStatic

Constant-height tree cut
collectGarbage

Iterative garbage collection.
labelPoints

Label scatterplot points
projectiveKMeans

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

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

Fast colunm-wise quantile of a matrix.
goodSamplesGenesMS

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

Merge modules and reassign genes using kME.
TOMsimilarityFromExpr

Topological overlap matrix
chooseTopHubInEachModule

Chooses the top hub gene in each module
automaticNetworkScreening

One-step automatic network gene screening
goodGenesMS

Filter genes with too many missing entries across multiple sets
consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.
consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering
sigmoidAdjacencyFunction

Sigmoid-type adacency function.
dynamicMergeCut

Threshold for module merging
modulePreservation

Calculation of module preservation statistics
Inline display of progress

Inline display of progress
vectorTOM

Topological overlap for a subset of the whole set of genes
adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression
matchLabels

Relabel module labels to best match the given reference labels
labeledHeatmap

Produce a labeled heatmap plot
subsetTOM

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

Hard-thresholding adjacency function
nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors
standardScreeningBinaryTrait

Standard screening for binatry traits
pickSoftThreshold

Analysis of scale free topology for soft-thresholding
GOenrichmentAnalysis

Calculation of GO enrichment (experimental)
matrixToNetwork

Construct a network from a matrix
networkConcepts

Calculations of network concepts
preservationNetworkConnectivity

Network preservation calculations
stratifiedBarplot

Bar plots of data across two splitting parameters
adjacency.polyReg

Adjacency matrix based on polynomial regression
moduleEigengenes

Calculate module eigengenes.
recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data
TOMsimilarity

Topological overlap matrix similarity and dissimilarity
nPresent

Number of present data entries.
blockwiseConsensusModules

Find consensus modules across several datasets.
adjacency

Calculate network adjacency
corPvalueFisher

Fisher's asymptotic p-value for correlation
conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.
plotModuleSignificance

Barplot of module significance
plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples
cor

Fast calculations of Pearson correlation.
cutreeStaticColor

Constant height tree cut using color labels
plot.mat

Red and Green Color Image of Data Matrix
consensusOrderMEs

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

Align expression data with given vector
signedKME

Signed eigengene-based connectivity
clusterCoef

Clustering coefficient calculation
plotColorUnderTree

Plot color rows under a dendrogram
setCorrelationPreservation

Summary correlation preservation measure
moduleNumber

Fixed-height cut of a dendrogram.
vectorizeMatrix

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

Rand index of two partitions
unsignedAdjacency

Calculation of unsigned adjacency
coClustering.permutationTest

Permutation test for co-clustering
labeledBarplot

Barplot with text or color labels.
hubGeneSignificance

Hubgene significance
standardScreeningNumericTrait

Standard screening for numeric traits
WGCNA-package

Weighted Gene Co-Expression Network Analysis
exportNetworkToCytoscape

Export network to Cytoscape
TOMplot

Graphical representation of the Topological Overlap Matrix
stat.bwss

Between and Within Group Sum of Squares Calculation
scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.
labels2colors

Convert numerical labels to colors.
accuracyMeasures

Accuracy measures for a 2x2 confusion matrix.
prepComma

Prepend a comma to a non-empty string
nearestCentroidPredictor

Nearest centroid predictor
mergeCloseModules

Merge close modules in gene expression data
AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
checkAdjMat

Check adjacency matrix
corPredictionSuccess

Qunatification of success of gene screening
bicor

Biweight Midcorrelation
correlationPreservation

Preservation of eigengene correlations
displayColors

Show colors used to label modules
plotNetworkHeatmap

Network heatmap plot
goodSamplesGenes

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

Colors this library uses for labeling modules.
rgcolors.func

Red and Green Color Specification
coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model
recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data
coClustering

Co-clustering measure of cluster preservation between two clusterings
networkScreening

Identification of genes related to a trait
bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values
goodSamplesMS

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

Network gene screening with an external gene significance measure
exportNetworkToVisANT

Export network data in format readable by VisANT
orderMEs

Put close eigenvectors next to each other
pquantile

Parallel quantile, median, mean
softConnectivity

Calculates connectivity of a weighted network.
stdErr

Standard error of the mean of a given vector.
populationMeansInAdmixture

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

Select one representative row per group
goodSamples

Filter samples with too many missing entries
intramodularConnectivity

Calculation of intramodular connectivity
rankPvalue

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

Keep probes that are shared among given data sets
greenBlackRed

Green-black-red color sequence
votingLinearPredictor

Voting linear predictor
standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable
simulateModule

Simulate a gene co-expression module
propVarExplained

Proportion of variance explained by eigengenes.
plotEigengeneNetworks

Eigengene network plot
proportionsInAdmixture

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

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

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

Selects one representative row per group based on kME
stat.diag.da

Diagonal Discriminant Analysis
chooseOneHubInEachModule

Chooses a single hub gene in each module
consensusProjectiveKMeans

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

Dendrogram plot with color annotation of objects
numbers2colors

Color representation for a numeric variable
qvalue

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

Compare prediction success
metaZfunction

Meta-analysis Z statistic
fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.
removePrincipalComponents

Remove leading principal components from data
simulateMultiExpr

Simulate multi-set expression data
mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information
overlapTable

Calculate overlap of modules
spaste

Space-less paste
simulateDatExpr

Simulation of expression data
nearestNeighborConnectivityMS

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

Transform numerical labels into normal order.
verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value
simulateDatExpr5Modules

Simplified simulation of expression data
orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.
scaleFreePlot

Visual check of scale-free topology
corAndPvalue

Calculation of correlations and associated p-values
removeGreyME

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

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

Filter genes with too many missing entries
pickHardThreshold

Analysis of scale free topology for hard-thresholding.
corPvalueStudent

Student asymptotic p-value for correlation
na

Basic Statistical Functions for Handling Missing Values
multiSetMEs

Calculate module eigengenes.
overlapTableUsingKME

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

Pairwise scatterplots of eigengenes
sizeGrWindow

Opens a graphics window with specified dimensions
verboseScatterplot

Scatterplot annotated by regression line and p-value
GTOMdist

Generalized Topological Overlap Measure
addTraitToMEs

Add trait information to multi-set module eigengene structure
blockwiseModules

Automatic network construction and module detection
kMEcomparisonScatterplot

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

Red-white-green color sequence
simulateSmallLayer

Simulate small modules
automaticNetworkScreeningGS

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

Add grid lines to an existing plot.
checkSets

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

Green-white-red color sequence
moduleColor.getMEprefix

Get the prefix used to label module eigengenes.
plot.cor

Red and Green Color Image of Correlation Matrix
simulateEigengeneNetwork

Simulate eigengene network from a causal model
userListEnrichment

Measure enrichment between inputted and user-defined lists