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WGCNA (version 1.15)

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

1.15

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

November 12th, 2011

Functions in WGCNA (1.15)

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

coClustering

Co-clustering measure of cluster preservation between two clusterings

conformityDecomposition

Conformity and module based decomposition of a network adjacency matrix.

plotMat

Red and Green Color Image of Data Matrix

checkAdjMat

Check adjacency matrix

simulateDatExpr

Simulation of expression data

multiSetMEs

Calculate module eigengenes.

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

standardColors

Colors this library uses for labeling modules.

standardScreeningNumericTrait

Standard screening for numeric traits

coClustering.permutationTest

Permutation test for co-clustering

cor

Fast calculations of Pearson correlation.

nearestCentroidPredictor

Nearest centroid predictor

cutreeStatic

Constant-height tree cut

userListEnrichment

Measure enrichment between inputted and user-defined lists

displayColors

Show colors used to label modules

addTraitToMEs

Add trait information to multi-set module eigengene structure

colQuantileC

Fast colunm-wise quantile of a matrix.

softConnectivity

Calculates connectivity of a weighted network.

dynamicMergeCut

Threshold for module merging

SCsLists

Stem Cell-Related Genes with Corresponding Gene Markers

adjacency

Calculate network adjacency

corPredictionSuccess

Qunatification of success of gene screening

accuracyMeasures

Accuracy measures for a 2x2 confusion matrix.

stdErr

Standard error of the mean of a given vector.

collapseRows

Select one representative row per group

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

goodSamples

Filter samples with too many missing entries

plotDendroAndColors

Dendrogram plot with color annotation of objects

collapseRowsUsingKME

Selects one representative row per group based on kME

unsignedAdjacency

Calculation of unsigned adjacency

nPresent

Number of present data entries.

collectGarbage

Iterative garbage collection.

metaAnalysis

Meta-analysis of binary and continuous variables

networkScreening

Identification of genes related to a trait

overlapTableUsingKME

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

blockwiseModules

Automatic network construction and module detection

plotColorUnderTree

Plot color rows under a dendrogram

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

corAndPvalue

Calculation of correlations and associated p-values

exportNetworkToCytoscape

Export network to Cytoscape

normalizeLabels

Transform numerical labels into normal order.

chooseOneHubInEachModule

Chooses a single hub gene in each module

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

matchLabels

Relabel module labels to best match the given reference labels

plotEigengeneNetworks

Eigengene network plot

corPvalueFisher

Fisher's asymptotic p-value for correlation

verboseIplot

Scatterplot with density

standardScreeningBinaryTrait

Standard screening for binatry traits

signedKME

Signed eigengene-based connectivity

fixDataStructure

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

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

chooseTopHubInEachModule

Chooses the top hub gene in each module

verboseBarplot

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

BloodLists

Blood Cell Types with Corresponding Gene Markers

intramodularConnectivity

Calculation of intramodular connectivity

multiData.eigengeneSignificance

Eigengene significance across multiple sets

consensusKME

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

GTOMdist

Generalized Topological Overlap Measure

numbers2colors

Color representation for a numeric variable

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

vectorTOM

Topological overlap for a subset of the whole set of genes

stratifiedBarplot

Bar plots of data across two splitting parameters

modulePreservation

Calculation of module preservation statistics

labeledBarplot

Barplot with text or color labels.

adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression

moduleMergeUsingKME

Merge modules and reassign genes using kME.

coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model

plotCor

Red and Green Color Image of Correlation Matrix

TOMplot

Graphical representation of the Topological Overlap Matrix

WGCNA-package

Weighted Gene Co-Expression Network Analysis

blockwiseConsensusModules

Find consensus modules across several datasets.

plotNetworkHeatmap

Network heatmap plot

stat.bwss

Between and Within Group Sum of Squares Calculation

automaticNetworkScreening

One-step automatic network gene screening

hubGeneSignificance

Hubgene significance

TOMsimilarityFromExpr

Topological overlap matrix

orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.

goodSamplesGenesMS

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

swapTwoBranches

Select, swap, or reflect branches in a dendrogram.

propVarExplained

Proportion of variance explained by eigengenes.

greenWhiteRed

Green-white-red color sequence

overlapTable

Calculate overlap of modules

projectiveKMeans

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

AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation

mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information

signumAdjacencyFunction

Hard-thresholding adjacency function

rgcolors.func

Red and Green Color Specification

checkSets

Check structure and retrieve sizes of a group of datasets.

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

BrainLists

Brain-Related Categories with Corresponding Gene Markers

labels2colors

Convert numerical labels to colors.

votingLinearPredictor

Voting linear predictor

corPvalueStudent

Student asymptotic p-value for correlation

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

verboseScatterplot

Scatterplot annotated by regression line and p-value

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

proportionsInAdmixture

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

goodGenesMS

Filter genes with too many missing entries across multiple sets

labeledHeatmap

Produce a labeled heatmap plot

redWhiteGreen

Red-white-green color sequence

alignExpr

Align expression data with given vector

labelPoints

Label scatterplot points

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

moduleEigengenes

Calculate module eigengenes.

metaZfunction

Meta-analysis Z statistic

nearestNeighborConnectivityMS

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

preservationNetworkConnectivity

Network preservation calculations

Basic Statistical Functions for Handling Missing Values

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.

simulateSmallLayer

Simulate small modules

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

Inline display of progress

consensusProjectiveKMeans

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

exportNetworkToVisANT

Export network data in format readable by VisANT

networkScreeningGS

Network gene screening with an external gene significance measure

addErrorBars

Add error bars to a barplot.

networkConcepts

Calculations of network concepts

plotMEpairs

Pairwise scatterplots of eigengenes

orderMEs

Put close eigenvectors next to each other

plotModuleSignificance

Barplot of module significance

qvalue

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

rankPvalue

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

simulateEigengeneNetwork

Simulate eigengene network from a causal model

relativeCorPredictionSuccess

Compare prediction success

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

qvalue.restricted

qvalue convenience wrapper

simulateModule

Simulate a gene co-expression module

spaste

Space-less paste

randIndex

Rand index of two partitions

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value

stat.diag.da

Diagonal Discriminant Analysis

clusterCoef

Clustering coefficient calculation

subsetTOM

Topological overlap for a subset of a whole set of genes

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

addGuideLines

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

greenBlackRed

Green-black-red color sequence

kMEcomparisonScatterplot

Function to plot kME values between two comparable data sets.

prepComma

Prepend a comma to a non-empty string

simulateDatExpr5Modules

Simplified simulation of expression data

allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations

addGrid

Add grid lines to an existing plot.

goodGenes

Filter genes with too many missing entries

keepCommonProbes

Keep probes that are shared among given data sets

populationMeansInAdmixture

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

pquantile

Parallel quantile, median, mean

scaleFreePlot

Visual check of scale-free topology

removePrincipalComponents

Remove leading principal components from data

simulateMultiExpr

Simulate multi-set expression data

sizeGrWindow

Opens a graphics window with specified dimensions

adjacency.polyReg

Adjacency matrix based on polynomial regression

bicor

Biweight Midcorrelation

consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

mergeCloseModules

Merge close modules in gene expression data

matrixToNetwork

Construct a network from a matrix

correlationPreservation

Preservation of eigengene correlations

setCorrelationPreservation

Summary correlation preservation measure

TOMsimilarity

Topological overlap matrix similarity and dissimilarity

moduleNumber

Fixed-height cut of a dendrogram.

cutreeStaticColor

Constant height tree cut using color labels