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WGCNA (version 1.20)

Weighted Correlation Network Analysis

Description

Functions necessary to perform Weighted Correlation Network Analysis

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Version

Install

install.packages('WGCNA')

Monthly Downloads

11,673

Version

1.20

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

April 24th, 2012

Functions in WGCNA (1.20)

consensusKME

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

TOMsimilarityFromExpr

Topological overlap matrix

adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

blockwiseModules

Automatic network construction and module detection

displayColors

Show colors used to label modules

TOMsimilarity

Topological overlap matrix similarity and dissimilarity

collectGarbage

Iterative garbage collection.

collapseRows

Select one representative row per group

clusterCoef

Clustering coefficient calculation

moduleMergeUsingKME

Merge modules and reassign genes using kME.

GTOMdist

Generalized Topological Overlap Measure

addGuideLines

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

labelPoints

Label scatterplot points

chooseOneHubInEachModule

Chooses a single hub gene in each module

consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering

SCsLists

Stem Cell-Related Genes with Corresponding Gene Markers

Inline display of progress

adjacency.polyReg

Adjacency matrix based on polynomial regression

networkConcepts

Calculations of network concepts

exportNetworkToVisANT

Export network data in format readable by VisANT

coClustering.permutationTest

Permutation test for co-clustering

colQuantileC

Fast colunm-wise quantile of a matrix.

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

nSets

Number of sets in a multi-set variable

exportNetworkToCytoscape

Export network to Cytoscape

consensusProjectiveKMeans

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

BloodLists

Blood Cell Types with Corresponding Gene Markers

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

matrixToNetwork

Construct a network from a matrix

AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation

addTraitToMEs

Add trait information to multi-set module eigengene structure

metaZfunction

Meta-analysis Z statistic

TrueTrait

Estimate the true trait underlying a list of surrogate markers.

checkAdjMat

Check adjacency matrix

hubGeneSignificance

Hubgene significance

collapseRowsUsingKME

Selects one representative row per group based on kME

consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.

coClustering

Co-clustering measure of cluster preservation between two clusterings

orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.

nearestNeighborConnectivityMS

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

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

kMEcomparisonScatterplot

Function to plot kME values between two comparable data sets.

corPvalueFisher

Fisher's asymptotic p-value for correlation

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

greenBlackRed

Green-black-red color sequence

checkSets

Check structure and retrieve sizes of a group of datasets.

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

metaAnalysis

Meta-analysis of binary and continuous variables

blockwiseIndividualTOMs

Calculation of block-wise topological overlaps

modulePreservation

Calculation of module preservation statistics

labeledBarplot

Barplot with text or color labels.

intramodularConnectivity

Calculation of intramodular connectivity

BrainLists

Brain-Related Categories with Corresponding Gene Markers

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

blockwiseConsensusModules

Find consensus modules across several datasets.

chooseTopHubInEachModule

Chooses the top hub gene in each module

plotDendroAndColors

Dendrogram plot with color annotation of objects

conformityDecomposition

Conformity and module based decomposition of a network adjacency matrix.

stat.bwss

Between and Within Group Sum of Squares Calculation

standardScreeningBinaryTrait

Standard screening for binatry traits

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

keepCommonProbes

Keep probes that are shared among given data sets

prepComma

Prepend a comma to a non-empty string

cutreeStatic

Constant-height tree cut

nPresent

Number of present data entries.

correlationPreservation

Preservation of eigengene correlations

normalizeLabels

Transform numerical labels into normal order.

TOMplot

Graphical representation of the Topological Overlap Matrix

simulateDatExpr5Modules

Simplified simulation of expression data

mergeCloseModules

Merge close modules in gene expression data

stratifiedBarplot

Bar plots of data across two splitting parameters

pquantile

Parallel quantile, median, mean

qvalue

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

bicor

Biweight Midcorrelation

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

automaticNetworkScreening

One-step automatic network gene screening

softConnectivity

Calculates connectivity of a weighted network.

signumAdjacencyFunction

Hard-thresholding adjacency function

labeledHeatmap

Produce a labeled heatmap plot

corPvalueStudent

Student asymptotic p-value for correlation

multiData.eigengeneSignificance

Eigengene significance across multiple sets

blueWhiteRed

Blue-white-red color sequence

numbers2colors

Color representation for a numeric variable

accuracyMeasures

Accuracy measures for a 2x2 confusion matrix.

overlapTableUsingKME

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

votingLinearPredictor

Voting linear predictor

plotEigengeneNetworks

Eigengene network plot

dynamicMergeCut

Threshold for module merging

userListEnrichment

Measure enrichment between inputted and user-defined lists

allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations

Basic Statistical Functions for Handling Missing Values

cutreeStaticColor

Constant height tree cut using color labels

plotColorUnderTree

Plot color rows under a dendrogram

WGCNA-package

Weighted Gene Co-Expression Network Analysis

labels2colors

Convert numerical labels to colors.

goodGenes

Filter genes with too many missing entries

simulateDatExpr

Simulation of expression data

stat.diag.da

Diagonal Discriminant Analysis

projectiveKMeans

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

cor

Fast calculations of Pearson correlation.

corPredictionSuccess

Qunatification of success of gene screening

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

adjacency

Calculate network adjacency

multiSetMEs

Calculate module eigengenes.

fixDataStructure

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

alignExpr

Align expression data with given vector

networkScreeningGS

Network gene screening with an external gene significance measure

overlapTable

Calculate overlap of modules

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

plotModuleSignificance

Barplot of module significance

mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information

networkScreening

Identification of genes related to a trait

moduleNumber

Fixed-height cut of a dendrogram.

orderMEs

Put close eigenvectors next to each other

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

standardColors

Colors this library uses for labeling modules.

relativeCorPredictionSuccess

Compare prediction success

nearestCentroidPredictor

Nearest centroid predictor

qvalue.restricted

qvalue convenience wrapper

plotNetworkHeatmap

Network heatmap plot

simulateEigengeneNetwork

Simulate eigengene network from a causal model

sizeGrWindow

Opens a graphics window with specified dimensions

proportionsInAdmixture

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

goodSamples

Filter samples with too many missing entries

vectorTOM

Topological overlap for a subset of the whole set of genes

simulateMultiExpr

Simulate multi-set expression data

removePrincipalComponents

Remove leading principal components from data

propVarExplained

Proportion of variance explained by eigengenes.

verboseIplot

Scatterplot with density

moduleEigengenes

Calculate module eigengenes.

plotMat

Red and Green Color Image of Data Matrix

lowerTri2matrix

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

unsignedAdjacency

Calculation of unsigned adjacency

simulateSmallLayer

Simulate small modules

goodSamplesGenesMS

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

simulateModule

Simulate a gene co-expression module

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

rankPvalue

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

verboseScatterplot

Scatterplot annotated by regression line and p-value

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

populationMeansInAdmixture

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

subsetTOM

Topological overlap for a subset of a whole set of genes

coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model

scaleFreePlot

Visual check of scale-free topology

setCorrelationPreservation

Summary correlation preservation measure

signedKME

Signed eigengene-based connectivity

greenWhiteRed

Green-white-red color sequence

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

redWhiteGreen

Red-white-green color sequence

plotMEpairs

Pairwise scatterplots of eigengenes

swapTwoBranches

Select, swap, or reflect branches in a dendrogram.

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

preservationNetworkConnectivity

Network preservation calculations

verboseBarplot

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

standardScreeningNumericTrait

Standard screening for numeric traits

rgcolors.func

Red and Green Color Specification

spaste

Space-less paste

stdErr

Standard error of the mean of a given vector.

plotCor

Red and Green Color Image of Correlation Matrix

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

addErrorBars

Add error bars to a barplot.

addGrid

Add grid lines to an existing plot.

corAndPvalue

Calculation of correlations and associated p-values

matchLabels

Relabel module labels to best match the given reference labels

randIndex

Rand index of two partitions

goodGenesMS

Filter genes with too many missing entries across multiple sets