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WGCNA (version 1.18-1)

Weighted Correlation Network Analysis

Description

Functions necessary to perform Weighted Correlation Network Analysis

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Install

install.packages('WGCNA')

Monthly Downloads

16,020

Version

1.18-1

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

January 5th, 2012

Functions in WGCNA (1.18-1)

TOMsimilarity

Topological overlap matrix similarity and dissimilarity

BrainLists

Brain-Related Categories with Corresponding Gene Markers

GTOMdist

Generalized Topological Overlap Measure

consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations

cor

Fast calculations of Pearson correlation.

correlationPreservation

Preservation of eigengene correlations

accuracyMeasures

Accuracy measures for a 2x2 confusion matrix.

blockwiseConsensusModules

Find consensus modules across several datasets.

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

metaZfunction

Meta-analysis Z statistic

displayColors

Show colors used to label modules

alignExpr

Align expression data with given vector

multiSetMEs

Calculate module eigengenes.

AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation

addGrid

Add grid lines to an existing plot.

collapseRowsUsingKME

Selects one representative row per group based on kME

chooseOneHubInEachModule

Chooses a single hub gene in each module

coClustering.permutationTest

Permutation test for co-clustering

plotDendroAndColors

Dendrogram plot with color annotation of objects

TOMplot

Graphical representation of the Topological Overlap Matrix

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

moduleNumber

Fixed-height cut of a dendrogram.

fixDataStructure

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

corPvalueFisher

Fisher's asymptotic p-value for correlation

adjacency

Calculate network adjacency

SCsLists

Stem Cell-Related Genes with Corresponding Gene Markers

addErrorBars

Add error bars to a barplot.

adjacency.polyReg

Adjacency matrix based on polynomial regression

addGuideLines

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

bicor

Biweight Midcorrelation

multiData.eigengeneSignificance

Eigengene significance across multiple sets

populationMeansInAdmixture

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

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

dynamicMergeCut

Threshold for module merging

colQuantileC

Fast colunm-wise quantile of a matrix.

networkScreening

Identification of genes related to a trait

cutreeStaticColor

Constant height tree cut using color labels

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

collectGarbage

Iterative garbage collection.

numbers2colors

Color representation for a numeric variable

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

collapseRows

Select one representative row per group

goodSamplesGenesMS

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

checkSets

Check structure and retrieve sizes of a group of datasets.

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

nearestNeighborConnectivityMS

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

plotModuleSignificance

Barplot of module significance

simulateDatExpr

Simulation of expression data

goodSamples

Filter samples with too many missing entries

consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

plotColorUnderTree

Plot color rows under a dendrogram

blockwiseModules

Automatic network construction and module detection

cutreeStatic

Constant-height tree cut

hubGeneSignificance

Hubgene significance

chooseTopHubInEachModule

Chooses the top hub gene in each module

coClustering

Co-clustering measure of cluster preservation between two clusterings

TOMsimilarityFromExpr

Topological overlap matrix

automaticNetworkScreening

One-step automatic network gene screening

overlapTableUsingKME

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

matrixToNetwork

Construct a network from a matrix

consensusKME

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

goodGenesMS

Filter genes with too many missing entries across multiple sets

plotCor

Red and Green Color Image of Correlation Matrix

intramodularConnectivity

Calculation of intramodular connectivity

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

redWhiteGreen

Red-white-green color sequence

corPredictionSuccess

Qunatification of success of gene screening

greenWhiteRed

Green-white-red color sequence

consensusProjectiveKMeans

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

matchLabels

Relabel module labels to best match the given reference labels

projectiveKMeans

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

labels2colors

Convert numerical labels to colors.

addTraitToMEs

Add trait information to multi-set module eigengene structure

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.

checkAdjMat

Check adjacency matrix

orderMEs

Put close eigenvectors next to each other

proportionsInAdmixture

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

swapTwoBranches

Select, swap, or reflect branches in a dendrogram.

standardScreeningNumericTrait

Standard screening for numeric traits

keepCommonProbes

Keep probes that are shared among given data sets

signumAdjacencyFunction

Hard-thresholding adjacency function

verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value

greenBlackRed

Green-black-red color sequence

rankPvalue

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

exportNetworkToVisANT

Export network data in format readable by VisANT

goodGenes

Filter genes with too many missing entries

kMEcomparisonScatterplot

Function to plot kME values between two comparable data sets.

userListEnrichment

Measure enrichment between inputted and user-defined lists

spaste

Space-less paste

labeledHeatmap

Produce a labeled heatmap plot

plotNetworkHeatmap

Network heatmap plot

BloodLists

Blood Cell Types with Corresponding Gene Markers

WGCNA-package

Weighted Gene Co-Expression Network Analysis

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

corAndPvalue

Calculation of correlations and associated p-values

corPvalueStudent

Student asymptotic p-value for correlation

mergeCloseModules

Merge close modules in gene expression data

metaAnalysis

Meta-analysis of binary and continuous variables

mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information

plotEigengeneNetworks

Eigengene network plot

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

simulateDatExpr5Modules

Simplified simulation of expression data

propVarExplained

Proportion of variance explained by eigengenes.

networkScreeningGS

Network gene screening with an external gene significance measure

rgcolors.func

Red and Green Color Specification

standardScreeningBinaryTrait

Standard screening for binatry traits

qvalue.restricted

qvalue convenience wrapper

Inline display of progress

conformityDecomposition

Conformity and module based decomposition of a network adjacency matrix.

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

qvalue

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

randIndex

Rand index of two partitions

labeledBarplot

Barplot with text or color labels.

labelPoints

Label scatterplot points

softConnectivity

Calculates connectivity of a weighted network.

nPresent

Number of present data entries.

plotMat

Red and Green Color Image of Data Matrix

preservationNetworkConnectivity

Network preservation calculations

stdErr

Standard error of the mean of a given vector.

relativeCorPredictionSuccess

Compare prediction success

prepComma

Prepend a comma to a non-empty string

simulateModule

Simulate a gene co-expression module

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

votingLinearPredictor

Voting linear predictor

verboseScatterplot

Scatterplot annotated by regression line and p-value

sizeGrWindow

Opens a graphics window with specified dimensions

networkConcepts

Calculations of network concepts

subsetTOM

Topological overlap for a subset of a whole set of genes

unsignedAdjacency

Calculation of unsigned adjacency

simulateEigengeneNetwork

Simulate eigengene network from a causal model

stat.diag.da

Diagonal Discriminant Analysis

simulateMultiExpr

Simulate multi-set expression data

stat.bwss

Between and Within Group Sum of Squares Calculation

exportNetworkToCytoscape

Export network to Cytoscape

stratifiedBarplot

Bar plots of data across two splitting parameters

vectorTOM

Topological overlap for a subset of the whole set of genes

overlapTable

Calculate overlap of modules

pquantile

Parallel quantile, median, mean

Basic Statistical Functions for Handling Missing Values

plotMEpairs

Pairwise scatterplots of eigengenes

moduleEigengenes

Calculate module eigengenes.

clusterCoef

Clustering coefficient calculation

scaleFreePlot

Visual check of scale-free topology

simulateSmallLayer

Simulate small modules

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

modulePreservation

Calculation of module preservation statistics

verboseIplot

Scatterplot with density

verboseBarplot

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

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

removePrincipalComponents

Remove leading principal components from data

setCorrelationPreservation

Summary correlation preservation measure

standardColors

Colors this library uses for labeling modules.

adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression

coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model

moduleMergeUsingKME

Merge modules and reassign genes using kME.

nearestCentroidPredictor

Nearest centroid predictor

normalizeLabels

Transform numerical labels into normal order.

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

signedKME

Signed eigengene-based connectivity