Learn R Programming
⚠️There's a newer version (1.73) of this package.Take me there.

WGCNA (version 1.10-2)

Weighted Gene Co-Expression Network Analysis

Description

Functions necessary to perform Weighted Gene Co-Expression Network Analysis

Copy Link

Version

Install

install.packages('WGCNA')

Monthly Downloads

13,041

Version

1.10-2

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

April 24th, 2011

Functions in WGCNA (1.10-2)

addGuideLines

Add vertical ``guide lines'' to a dendrogram plot
moduleColor.getMEprefix

Get the prefix used to label module eigengenes.
TOMsimilarityFromExpr

Topological overlap matrix
pquantile

Parallel quantile, median, mean
blockwiseModules

Automatic network construction and module detection
alignExpr

Align expression data with given vector
automaticNetworkScreening

One-step automatic network gene screening
AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
addTraitToMEs

Add trait information to multi-set module eigengene structure
networkConcepts

Calculations of network concepts
scaleFreePlot

Visual check of scale-free topology
dynamicMergeCut

Threshold for module merging
nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors
cor

Fast calculations of Pearson correlation.
BrainLists

Brain-Related Categories with Corresponding Gene Markers
TOMsimilarity

Topological overlap matrix similarity and dissimilarity
orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.
Inline display of progress

Inline display of progress
blockwiseConsensusModules

Find consensus modules across several datasets.
matchLabels

Relabel module labels to best match the given reference labels
bicor

Biweight Midcorrelation
labeledBarplot

Barplot with text or color labels.
goodSamples

Filter samples with too many missing entries
goodSamplesMS

Filter samples with too many missing entries across multiple data sets
adjacency.polyReg

Adjacency matrix based on polynomial regression
moduleNumber

Fixed-height cut of a dendrogram.
GTOMdist

Generalized Topological Overlap Measure
stratifiedBarplot

Bar plots of data across two splitting parameters
fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.
automaticNetworkScreeningGS

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

Fisher's asymptotic p-value for correlation
subsetTOM

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

Check adjacency matrix
preservationNetworkConnectivity

Network preservation calculations
accuracyMeasures

Accuracy measures for a 2x2 confusion matrix.
adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression
hubGeneSignificance

Hubgene significance
bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values
multiSetMEs

Calculate module eigengenes.
conformityDecomposition

Conformity vector(s) and factorizability measure(s) of a network
moduleMergeUsingKME

Merge modules and reassign genes using kME.
mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information
goodSamplesGenesMS

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

Filter genes with too many missing entries across multiple sets
fixDataStructure

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

Barplot of module significance
exportNetworkToCytoscape

Export network to Cytoscape
coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model
numbers2colors

Color representation for a numeric variable
populationMeansInAdmixture

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

Identification of genes related to a trait
networkScreeningGS

Network gene screening with an external gene significance measure
plotColorUnderTree

Plot color rows under a dendrogram
consensusOrderMEs

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

Co-clustering measure of cluster preservation between two clusterings
mergeCloseModules

Merge close modules in gene expression data
cutreeStaticColor

Constant height tree cut using color labels
modulePreservation

Calculation of module preservation statistics
corAndPvalue

Calculation of correlations and associated p-values
matrixToNetwork

Construct a network from a matrix
nearestNeighborConnectivityMS

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

Add error bars to a barplot.
plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples
exportNetworkToVisANT

Export network data in format readable by VisANT
chooseTopHubInEachModule

Chooses the top hub gene in each module
rankPvalue

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

Network heatmap plot
simulateEigengeneNetwork

Simulate eigengene network from a causal model
WGCNA-package

Weighted Gene Co-Expression Network Analysis
standardScreeningNumericTrait

Standard screening for numeric traits
stat.diag.da

Diagonal Discriminant Analysis
swapTwoBranches

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

Consensus dissimilarity of module eigengenes.
rgcolors.func

Red and Green Color Specification
cutreeStatic

Constant-height tree cut
simulateSmallLayer

Simulate small modules
sizeGrWindow

Opens a graphics window with specified dimensions
simulateDatExpr5Modules

Simplified simulation of expression data
clusterCoef

Clustering coefficient calculation
collectGarbage

Iterative garbage collection.
standardColors

Colors this library uses for labeling modules.
simulateDatExpr

Simulation of expression data
collapseRows

Select one representative row per group
addGrid

Add grid lines to an existing plot.
coClustering.permutationTest

Permutation test for co-clustering
plotMEpairs

Pairwise scatterplots of eigengenes
displayColors

Show colors used to label modules
checkSets

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

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

Selects one representative row per group based on kME
redWhiteGreen

Red-white-green color sequence
metaZfunction

Meta-analysis Z statistic
goodGenes

Filter genes with too many missing entries
consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering
labelPoints

Label scatterplot points
pickHardThreshold

Analysis of scale free topology for hard-thresholding.
goodSamplesGenes

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

Student asymptotic p-value for correlation
BloodLists

Blood Cell Types with Corresponding Gene Markers
moduleEigengenes

Calculate module eigengenes.
kMEcomparisonScatterplot

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

Green-white-red color sequence
GOenrichmentAnalysis

Calculation of GO enrichment (experimental)
normalizeLabels

Transform numerical labels into normal order.
adjacency

Calculate network adjacency
labels2colors

Convert numerical labels to colors.
colQuantileC

Fast colunm-wise quantile of a matrix.
na

Basic Statistical Functions for Handling Missing Values
correlationPreservation

Preservation of eigengene correlations
nPresent

Number of present data entries.
plotEigengeneNetworks

Eigengene network plot
greenBlackRed

Green-black-red color sequence
corPredictionSuccess

Qunatification of success of gene screening
setCorrelationPreservation

Summary correlation preservation measure
keepCommonProbes

Keep probes that are shared among given data sets
pickSoftThreshold

Analysis of scale free topology for soft-thresholding
recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data
verboseBarplot

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

Prepend a comma to a non-empty string
removeGreyME

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

Produce a labeled heatmap plot
relativeCorPredictionSuccess

Compare prediction success
spaste

Space-less paste
overlapTable

Calculate overlap of modules
chooseOneHubInEachModule

Chooses a single hub gene in each module
stdErr

Standard error of the mean of a given vector.
randIndex

Rand index of two partitions
sigmoidAdjacencyFunction

Sigmoid-type adacency function.
unsignedAdjacency

Calculation of unsigned adjacency
stat.bwss

Between and Within Group Sum of Squares Calculation
standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable
signedKME

Signed eigengene-based connectivity
userListEnrichment

Measure enrichment between inputted and user-defined lists
simulateMultiExpr

Simulate multi-set expression data
nearestCentroidPredictor

Nearest centroid predictor
recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data
projectiveKMeans

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

Scatterplot annotated by regression line and p-value
removePrincipalComponents

Remove leading principal components from data
scaleFreeFitIndex

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

Red and Green Color Image of Correlation Matrix
propVarExplained

Proportion of variance explained by eigengenes.
conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.
consensusProjectiveKMeans

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

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

Red and Green Color Image of Data Matrix
plotDendroAndColors

Dendrogram plot with color annotation of objects
votingLinearPredictor

Voting linear predictor
vectorizeMatrix

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

Simulate a gene co-expression module
vectorTOM

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

Hard-thresholding adjacency function
softConnectivity

Calculates connectivity of a weighted network.
TOMplot

Graphical representation of the Topological Overlap Matrix
intramodularConnectivity

Calculation of intramodular connectivity
orderMEs

Put close eigenvectors next to each other
proportionsInAdmixture

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

Standard screening for binatry traits
verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value