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WGCNA (version 1.22)

Weighted Correlation Network Analysis

Description

Functions necessary to perform Weighted Correlation Network Analysis

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Version

Install

install.packages('WGCNA')

Monthly Downloads

16,020

Version

1.22

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

June 19th, 2012

Functions in WGCNA (1.22)

TrueTrait

Estimate the true trait underlying a list of surrogate markers.

BloodLists

Blood Cell Types with Corresponding Gene Markers

blockwiseModules

Automatic network construction and module detection

bicor

Biweight Midcorrelation

adjacency.polyReg

Adjacency matrix based on polynomial regression

adjacency

Calculate network adjacency

checkAdjMat

Check adjacency matrix

allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations

chooseTopHubInEachModule

Chooses the top hub gene in each module

addErrorBars

Add error bars to a barplot.

consensusKME

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

consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

TOMsimilarityFromExpr

Topological overlap matrix

alignExpr

Align expression data with given vector

coClustering.permutationTest

Permutation test for co-clustering

conformityDecomposition

Conformity and module based decomposition of a network adjacency matrix.

AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation

blueWhiteRed

Blue-white-red color sequence

consensusProjectiveKMeans

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

corPvalueStudent

Student asymptotic p-value for correlation

consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering

collectGarbage

Iterative garbage collection.

blockwiseConsensusModules

Find consensus modules across several datasets.

corPredictionSuccess

Qunatification of success of gene screening

exportNetworkToCytoscape

Export network to Cytoscape

BrainLists

Brain-Related Categories with Corresponding Gene Markers

SCsLists

Stem Cell-Related Genes with Corresponding Gene Markers

goodGenes

Filter genes with too many missing entries

addTraitToMEs

Add trait information to multi-set module eigengene structure

cor

Fast calculations of Pearson correlation.

checkSets

Check structure and retrieve sizes of a group of datasets.

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

goodSamplesGenesMS

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

addGrid

Add grid lines to an existing plot.

blockwiseIndividualTOMs

Calculation of block-wise topological overlaps

GTOMdist

Generalized Topological Overlap Measure

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

coClustering

Co-clustering measure of cluster preservation between two clusterings

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

mergeCloseModules

Merge close modules in gene expression data

labeledBarplot

Barplot with text or color labels.

moduleEigengenes

Calculate module eigengenes.

WGCNA-package

Weighted Gene Co-Expression Network Analysis

cutreeStaticColor

Constant height tree cut using color labels

labeledHeatmap

Produce a labeled heatmap plot

matrixToNetwork

Construct a network from a matrix

TOMplot

Graphical representation of the Topological Overlap Matrix

labelPoints

Label scatterplot points

plotDendroAndColors

Dendrogram plot with color annotation of objects

cutreeStatic

Constant-height tree cut

corAndPvalue

Calculation of correlations and associated p-values

correlationPreservation

Preservation of eigengene correlations

keepCommonProbes

Keep probes that are shared among given data sets

exportNetworkToVisANT

Export network data in format readable by VisANT

intramodularConnectivity

Calculation of intramodular connectivity

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

simulateModule

Simulate a gene co-expression module

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

scaleFreePlot

Visual check of scale-free topology

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

nearestNeighborConnectivityMS

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

networkConcepts

Calculations of network concepts

projectiveKMeans

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

coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model

signedKME

Signed eigengene-based connectivity

goodSamples

Filter samples with too many missing entries

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

removePrincipalComponents

Remove leading principal components from data

metaZfunction

Meta-analysis Z statistic

modulePreservation

Calculation of module preservation statistics

displayColors

Show colors used to label modules

randIndex

Rand index of two partitions

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

goodGenesMS

Filter genes with too many missing entries across multiple sets

overlapTableUsingKME

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

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

multiSetMEs

Calculate module eigengenes.

greenBlackRed

Green-black-red color sequence

moduleNumber

Fixed-height cut of a dendrogram.

simulateMultiExpr

Simulate multi-set expression data

qvalue

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

simulateDatExpr

Simulation of expression data

mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information

fixDataStructure

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

spaste

Space-less paste

labels2colors

Convert numerical labels to colors.

metaAnalysis

Meta-analysis of binary and continuous variables

Inline display of progress

colQuantileC

Fast colunm-wise quantile of a matrix.

rankPvalue

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

collapseRows

Select one representative row per group

orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.

propVarExplained

Proportion of variance explained by eigengenes.

populationMeansInAdmixture

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

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

lowerTri2matrix

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

swapTwoBranches

Select, swap, or reflect branches in a dendrogram.

proportionsInAdmixture

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

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

standardScreeningNumericTrait

Standard screening for numeric traits

plotMat

Red and Green Color Image of Data Matrix

stat.bwss

Between and Within Group Sum of Squares Calculation

greenWhiteRed

Green-white-red color sequence

prepComma

Prepend a comma to a non-empty string

nPresent

Number of present data entries.

kMEcomparisonScatterplot

Function to plot kME values between two comparable data sets.

plotColorUnderTree

Plot color rows under a dendrogram

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

rgcolors.func

Red and Green Color Specification

preservationNetworkConnectivity

Network preservation calculations

hubGeneSignificance

Hubgene significance

stdErr

Standard error of the mean of a given vector.

nSets

Number of sets in a multi-set variable

vectorTOM

Topological overlap for a subset of the whole set of genes

plotModuleSignificance

Barplot of module significance

plotMEpairs

Pairwise scatterplots of eigengenes

simulateSmallLayer

Simulate small modules

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

setCorrelationPreservation

Summary correlation preservation measure

addGuideLines

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

orderMEs

Put close eigenvectors next to each other

stat.diag.da

Diagonal Discriminant Analysis

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

qvalue.restricted

qvalue convenience wrapper

collapseRowsUsingKME

Selects one representative row per group based on kME

pquantile

Parallel quantile, median, mean

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

simulateEigengeneNetwork

Simulate eigengene network from a causal model

verboseIplot

Scatterplot with density

sizeGrWindow

Opens a graphics window with specified dimensions

votingLinearPredictor

Voting linear predictor

redWhiteGreen

Red-white-green color sequence

plotNetworkHeatmap

Network heatmap plot

accuracyMeasures

Accuracy measures for a 2x2 confusion matrix.

standardColors

Colors this library uses for labeling modules.

dynamicMergeCut

Threshold for module merging

signumAdjacencyFunction

Hard-thresholding adjacency function

verboseScatterplot

Scatterplot annotated by regression line and p-value

stratifiedBarplot

Bar plots of data across two splitting parameters

subsetTOM

Topological overlap for a subset of a whole set of genes

networkScreeningGS

Network gene screening with an external gene significance measure

verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value

networkScreening

Identification of genes related to a trait

plotCor

Red and Green Color Image of Correlation Matrix

softConnectivity

Calculates connectivity of a weighted network.

verboseBarplot

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

adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression

corPvalueFisher

Fisher's asymptotic p-value for correlation

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

overlapTable

Calculate overlap of modules

standardScreeningBinaryTrait

Standard screening for binatry traits

unsignedAdjacency

Calculation of unsigned adjacency

userListEnrichment

Measure enrichment between inputted and user-defined lists

TOMsimilarity

Topological overlap matrix similarity and dissimilarity

chooseOneHubInEachModule

Chooses a single hub gene in each module

multiData.eigengeneSignificance

Eigengene significance across multiple sets

numbers2colors

Color representation for a numeric variable

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

simulateDatExpr5Modules

Simplified simulation of expression data

automaticNetworkScreening

One-step automatic network gene screening

clusterCoef

Clustering coefficient calculation

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

Basic Statistical Functions for Handling Missing Values

moduleMergeUsingKME

Merge modules and reassign genes using kME.

nearestCentroidPredictor

Nearest centroid predictor

matchLabels

Relabel module labels to best match the given reference labels

normalizeLabels

Transform numerical labels into normal order.

plotEigengeneNetworks

Eigengene network plot

relativeCorPredictionSuccess

Compare prediction success