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WGCNA (version 1.27-1)

Weighted Correlation Network Analysis

Description

Functions necessary to perform Weighted Correlation Network Analysis.

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Version

Install

install.packages('WGCNA')

Monthly Downloads

16,961

Version

1.27-1

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

April 2nd, 2013

Functions in WGCNA (1.27-1)

lowerTri2matrix

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

Brain-Related Categories with Corresponding Gene Markers
coClustering.permutationTest

Permutation test for co-clustering
PWLists

Pathways with Corresponding Gene Markers - Compiled by Mike Palazzolo and Jim Wang from CHDI
automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance
qvalue.restricted

qvalue convenience wrapper
chooseOneHubInEachModule

Chooses a single hub gene in each module
consensusKME

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

Co-clustering measure of cluster preservation between two clusterings
fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.
dynamicMergeCut

Threshold for module merging
ImmunePathwayLists

Immune Pathways with Corresponding Gene Markers
consensusOrderMEs

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

Calculation of correlations and associated p-values
metaZfunction

Meta-analysis Z statistic
bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values
alignExpr

Align expression data with given vector
chooseTopHubInEachModule

Chooses the top hub gene in each module
consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.
goodSamplesMS

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

Calculation of GO enrichment (experimental)
collapseRows

Select one representative row per group
corPvalueFisher

Fisher's asymptotic p-value for correlation
Inline display of progress

Inline display of progress
numbers2colors

Color representation for a numeric variable
plotNetworkHeatmap

Network heatmap plot
pickSoftThreshold

Analysis of scale free topology for soft-thresholding
TOMsimilarity

Topological overlap matrix similarity and dissimilarity
overlapTableUsingKME

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

Simulate eigengene network from a causal model
simulateModule

Simulate a gene co-expression module
blockSize

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

Add trait information to multi-set module eigengene structure
AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
scaleFreePlot

Visual check of scale-free topology
fixDataStructure

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

Find consensus modules across several datasets.
rgcolors.func

Red and Green Color Specification
collectGarbage

Iterative garbage collection.
kMEcomparisonScatterplot

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

Calculate module eigengenes.
SCsLists

Stem Cell-Related Genes with Corresponding Gene Markers
TOMsimilarityFromExpr

Topological overlap matrix
projectiveKMeans

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

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

Selects one representative row per group based on kME
automaticNetworkScreening

One-step automatic network gene screening
redWhiteGreen

Red-white-green color sequence
moduleColor.getMEprefix

Get the prefix used to label module eigengenes.
greenWhiteRed

Green-white-red color sequence
sizeGrWindow

Opens a graphics window with specified dimensions
pickHardThreshold

Analysis of scale free topology for hard-thresholding.
proportionsInAdmixture

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

Calculation of module preservation statistics
cutreeStaticColor

Constant height tree cut using color labels
randomGLMpredictor

Random generalized linear model predictor
matrixToNetwork

Construct a network from a matrix
networkConcepts

Calculations of network concepts
spaste

Space-less paste
mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information
recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data
scaleFreeFitIndex

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

Barplot with text or color labels.
simulateDatExpr

Simulation of expression data
plotCor

Red and Green Color Image of Correlation Matrix
preservationNetworkConnectivity

Network preservation calculations
corPvalueStudent

Student asymptotic p-value for correlation
prepComma

Prepend a comma to a non-empty string
multiSetMEs

Calculate module eigengenes.
unsignedAdjacency

Calculation of unsigned adjacency
BloodLists

Blood Cell Types with Corresponding Gene Markers
rankPvalue

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

Measure enrichment between inputted and user-defined lists
TOMplot

Graphical representation of the Topological Overlap Matrix
signedKME

Signed eigengene-based connectivity
verboseBarplot

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

Calculates connectivity of a weighted network.
simulateSmallLayer

Simulate small modules
colQuantileC

Fast colunm-wise quantile of a matrix.
WGCNA-package

Weighted Gene Co-Expression Network Analysis
cor

Fast calculations of Pearson correlation.
metaAnalysis

Meta-analysis of binary and continuous variables
displayColors

Show colors used to label modules
plotDendroAndColors

Dendrogram plot with color annotation of objects
propVarExplained

Proportion of variance explained by eigengenes.
vectorTOM

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

Deviance- and martingale residuals from a Cox regression model
standardScreeningBinaryTrait

Standard screening for binatry traits
subsetTOM

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

Add grid lines to an existing plot.
qvalue

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

Calculation of conformity-based network concepts.
consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering
labelPoints

Label scatterplot points
stdErr

Standard error of the mean of a given vector.
matchLabels

Relabel module labels to best match the given reference labels
TrueTrait

Estimate the true trait underlying a list of surrogate markers.
returnGeneSetsAsList

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

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

Number of present data entries.
goodSamplesGenes

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

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

Repeat blockwise module detection from pre-calculated data
verboseIplot

Scatterplot with density
adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression
swapTwoBranches

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

Green-black-red color sequence
nSets

Number of sets in a multi-set variable
multiData.eigengeneSignificance

Eigengene significance across multiple sets
goodSamples

Filter samples with too many missing entries
accuracyMeasures

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

Calculation of intramodular connectivity
bicor

Biweight Midcorrelation
addErrorBars

Add error bars to a barplot.
moduleNumber

Fixed-height cut of a dendrogram.
relativeCorPredictionSuccess

Compare prediction success
simulateMultiExpr

Simulate multi-set expression data
sigmoidAdjacencyFunction

Sigmoid-type adacency function.
votingLinearPredictor

Voting linear predictor
orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.
vectorizeMatrix

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

Rand index of two partitions
stat.diag.da

Diagonal Discriminant Analysis
overlapTable

Calculate overlap of modules
plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples
setCorrelationPreservation

Summary correlation preservation measure
removeGreyME

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

Gene Markers for Regions of the Human Brain
removePrincipalComponents

Remove leading principal components from data
blockwiseIndividualTOMs

Calculation of block-wise topological overlaps
networkScreening

Identification of genes related to a trait
verboseScatterplot

Scatterplot annotated by regression line and p-value
plotMat

Red and Green Color Image of Data Matrix
allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations
allocateJobs

Divide tasks among workers
goodGenesMS

Filter genes with too many missing entries across multiple sets
blueWhiteRed

Blue-white-red color sequence
clusterCoef

Clustering coefficient calculation
adjacency

Calculate network adjacency
addGuideLines

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

Boxplot annotated by a Kruskal-Wallis p-value
exportNetworkToCytoscape

Export network to Cytoscape
adjacency.polyReg

Adjacency matrix based on polynomial regression
conformityDecomposition

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

Automatic network construction and module detection
labels2colors

Convert numerical labels to colors.
keepCommonProbes

Keep probes that are shared among given data sets
goodGenes

Filter genes with too many missing entries
goodSamplesGenesMS

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

Produce a labeled heatmap plot
plotModuleSignificance

Barplot of module significance
nearestCentroidPredictor

Nearest centroid predictor
plotColorUnderTree

Plot color rows under a dendrogram
correlationPreservation

Preservation of eigengene correlations
pquantile

Parallel quantile, median, mean
populationMeansInAdmixture

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

Transpose a big matrix or data frame
na

Basic Statistical Functions for Handling Missing Values
signumAdjacencyFunction

Hard-thresholding adjacency function
standardScreeningNumericTrait

Standard screening for numeric traits
standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable
simulateDatExpr5Modules

Simplified simulation of expression data
exportNetworkToVisANT

Export network data in format readable by VisANT
stat.bwss

Between and Within Group Sum of Squares Calculation
cutreeStatic

Constant-height tree cut
corPredictionSuccess

Qunatification of success of gene screening
networkScreeningGS

Network gene screening with an external gene significance measure
orderMEs

Put close eigenvectors next to each other
plotEigengeneNetworks

Eigengene network plot
stratifiedBarplot

Bar plots of data across two splitting parameters
GTOMdist

Generalized Topological Overlap Measure
hubGeneSignificance

Hubgene significance
mergeCloseModules

Merge close modules in gene expression data
moduleMergeUsingKME

Merge modules and reassign genes using kME.
nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors
plotMEpairs

Pairwise scatterplots of eigengenes
checkAdjMat

Check adjacency matrix
standardColors

Colors this library uses for labeling modules.
normalizeLabels

Transform numerical labels into normal order.