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WGCNA (version 1.12)

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

1.12

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

August 17th, 2011

Functions in WGCNA (1.12)

addGrid

Add grid lines to an existing plot.

TOMsimilarity

Topological overlap matrix similarity and dissimilarity

BloodLists

Blood Cell Types with Corresponding Gene Markers

collectGarbage

Iterative garbage collection.

cutreeStatic

Constant-height tree cut

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

clusterCoef

Clustering coefficient calculation

coClustering

Co-clustering measure of cluster preservation between two clusterings

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

displayColors

Show colors used to label modules

mergeCloseModules

Merge close modules in gene expression data

coClustering.permutationTest

Permutation test for co-clustering

pquantile

Parallel quantile, median, mean

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

rankPvalue

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

consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.

fixDataStructure

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

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

checkAdjMat

Check adjacency matrix

automaticNetworkScreening

One-step automatic network gene screening

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.

consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering

alignExpr

Align expression data with given vector

goodGenes

Filter genes with too many missing entries

setCorrelationPreservation

Summary correlation preservation measure

populationMeansInAdmixture

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

corPvalueStudent

Student asymptotic p-value for correlation

TOMplot

Graphical representation of the Topological Overlap Matrix

moduleNumber

Fixed-height cut of a dendrogram.

simulateDatExpr

Simulation of expression data

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression

cutreeStaticColor

Constant height tree cut using color labels

matchLabels

Relabel module labels to best match the given reference labels

greenWhiteRed

Green-white-red color sequence

coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model

simulateEigengeneNetwork

Simulate eigengene network from a causal model

overlapTableUsingKME

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

numbers2colors

Color representation for a numeric variable

keepCommonProbes

Keep probes that are shared among given data sets

plotMat

Red and Green Color Image of Data Matrix

dynamicMergeCut

Threshold for module merging

stat.bwss

Between and Within Group Sum of Squares Calculation

signedKME

Signed eigengene-based connectivity

multiSetMEs

Calculate module eigengenes.

verboseScatterplot

Scatterplot annotated by regression line and p-value

randIndex

Rand index of two partitions

stat.diag.da

Diagonal Discriminant Analysis

normalizeLabels

Transform numerical labels into normal order.

corPredictionSuccess

Qunatification of success of gene screening

exportNetworkToCytoscape

Export network to Cytoscape

goodSamplesGenesMS

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

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

userListEnrichment

Measure enrichment between inputted and user-defined lists

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

sizeGrWindow

Opens a graphics window with specified dimensions

propVarExplained

Proportion of variance explained by eigengenes.

labeledBarplot

Barplot with text or color labels.

kMEcomparisonScatterplot

Function to plot kME values between two comparable data sets.

orderMEs

Put close eigenvectors next to each other

stdErr

Standard error of the mean of a given vector.

corPvalueFisher

Fisher's asymptotic p-value for correlation

collapseRows

Select one representative row per group

blockwiseConsensusModules

Find consensus modules across several datasets.

addTraitToMEs

Add trait information to multi-set module eigengene structure

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

labeledHeatmap

Produce a labeled heatmap plot

nPresent

Number of present data entries.

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

plotDendroAndColors

Dendrogram plot with color annotation of objects

BrainLists

Brain-Related Categories with Corresponding Gene Markers

colQuantileC

Fast colunm-wise quantile of a matrix.

prepComma

Prepend a comma to a non-empty string

Inline display of progress

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

modulePreservation

Calculation of module preservation statistics

nearestCentroidPredictor

Nearest centroid predictor

redWhiteGreen

Red-white-green color sequence

removePrincipalComponents

Remove leading principal components from data

networkScreeningGS

Network gene screening with an external gene significance measure

addErrorBars

Add error bars to a barplot.

overlapTable

Calculate overlap of modules

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

stratifiedBarplot

Bar plots of data across two splitting parameters

correlationPreservation

Preservation of eigengene correlations

chooseOneHubInEachModule

Chooses a single hub gene in each module

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

proportionsInAdmixture

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

simulateMultiExpr

Simulate multi-set expression data

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

standardScreeningNumericTrait

Standard screening for numeric traits

WGCNA-package

Weighted Gene Co-Expression Network Analysis

hubGeneSignificance

Hubgene significance

votingLinearPredictor

Voting linear predictor

GTOMdist

Generalized Topological Overlap Measure

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

conformityDecomposition

Conformity and module based decomposition of a network adjacency matrix.

goodGenesMS

Filter genes with too many missing entries across multiple sets

mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information

checkSets

Check structure and retrieve sizes of a group of datasets.

blockwiseModules

Automatic network construction and module detection

chooseTopHubInEachModule

Chooses the top hub gene in each module

moduleMergeUsingKME

Merge modules and reassign genes using kME.

greenBlackRed

Green-black-red color sequence

intramodularConnectivity

Calculation of intramodular connectivity

moduleEigengenes

Calculate module eigengenes.

exportNetworkToVisANT

Export network data in format readable by VisANT

AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation

Basic Statistical Functions for Handling Missing Values

relativeCorPredictionSuccess

Compare prediction success

plotNetworkHeatmap

Network heatmap plot

plotEigengeneNetworks

Eigengene network plot

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

simulateSmallLayer

Simulate small modules

verboseBarplot

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

goodSamples

Filter samples with too many missing entries

accuracyMeasures

Accuracy measures for a 2x2 confusion matrix.

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

networkConcepts

Calculations of network concepts

matrixToNetwork

Construct a network from a matrix

metaZfunction

Meta-analysis Z statistic

consensusProjectiveKMeans

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

bicor

Biweight Midcorrelation

projectiveKMeans

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

softConnectivity

Calculates connectivity of a weighted network.

plotCor

Red and Green Color Image of Correlation Matrix

plotModuleSignificance

Barplot of module significance

simulateModule

Simulate a gene co-expression module

rgcolors.func

Red and Green Color Specification

swapTwoBranches

Select, swap, or reflect branches in a dendrogram.

scaleFreePlot

Visual check of scale-free topology

standardColors

Colors this library uses for labeling modules.

TOMsimilarityFromExpr

Topological overlap matrix

adjacency.polyReg

Adjacency matrix based on polynomial regression

cor

Fast calculations of Pearson correlation.

plotMEpairs

Pairwise scatterplots of eigengenes

standardScreeningBinaryTrait

Standard screening for binatry traits

vectorTOM

Topological overlap for a subset of the whole set of genes

signumAdjacencyFunction

Hard-thresholding adjacency function

collapseRowsUsingKME

Selects one representative row per group based on kME

nearestNeighborConnectivityMS

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

preservationNetworkConnectivity

Network preservation calculations

qvalue

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

verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value

spaste

Space-less paste

simulateDatExpr5Modules

Simplified simulation of expression data

addGuideLines

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

adjacency

Calculate network adjacency

corAndPvalue

Calculation of correlations and associated p-values

labels2colors

Convert numerical labels to colors.

networkScreening

Identification of genes related to a trait

plotColorUnderTree

Plot color rows under a dendrogram

subsetTOM

Topological overlap for a subset of a whole set of genes

unsignedAdjacency

Calculation of unsigned adjacency

labelPoints

Label scatterplot points