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WGCNA (version 1.18-2)

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

1.18-2

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

January 13th, 2012

Functions in WGCNA (1.18-2)

addGuideLines

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

alignExpr

Align expression data with given vector

addErrorBars

Add error bars to a barplot.

SCsLists

Stem Cell-Related Genes with Corresponding Gene Markers

GTOMdist

Generalized Topological Overlap Measure

TOMsimilarityFromExpr

Topological overlap matrix

addTraitToMEs

Add trait information to multi-set module eigengene structure

blockwiseModules

Automatic network construction and module detection

consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering

adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression

AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation

addGrid

Add grid lines to an existing plot.

allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations

accuracyMeasures

Accuracy measures for a 2x2 confusion matrix.

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.

coClustering

Co-clustering measure of cluster preservation between two clusterings

TOMplot

Graphical representation of the Topological Overlap Matrix

adjacency

Calculate network adjacency

consensusKME

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

corPredictionSuccess

Qunatification of success of gene screening

collapseRows

Select one representative row per group

goodSamplesGenesMS

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

automaticNetworkScreening

One-step automatic network gene screening

bicor

Biweight Midcorrelation

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

chooseOneHubInEachModule

Chooses a single hub gene in each module

exportNetworkToCytoscape

Export network to Cytoscape

adjacency.polyReg

Adjacency matrix based on polynomial regression

goodGenesMS

Filter genes with too many missing entries across multiple sets

multiData.eigengeneSignificance

Eigengene significance across multiple sets

corPvalueStudent

Student asymptotic p-value for correlation

metaZfunction

Meta-analysis Z statistic

greenWhiteRed

Green-white-red color sequence

hubGeneSignificance

Hubgene significance

plotEigengeneNetworks

Eigengene network plot

checkSets

Check structure and retrieve sizes of a group of datasets.

Basic Statistical Functions for Handling Missing Values

BrainLists

Brain-Related Categories with Corresponding Gene Markers

verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value

TOMsimilarity

Topological overlap matrix similarity and dissimilarity

collectGarbage

Iterative garbage collection.

clusterCoef

Clustering coefficient calculation

WGCNA-package

Weighted Gene Co-Expression Network Analysis

labelPoints

Label scatterplot points

conformityDecomposition

Conformity and module based decomposition of a network adjacency matrix.

BloodLists

Blood Cell Types with Corresponding Gene Markers

populationMeansInAdmixture

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

orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.

corAndPvalue

Calculation of correlations and associated p-values

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

fixDataStructure

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

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

coClustering.permutationTest

Permutation test for co-clustering

coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model

checkAdjMat

Check adjacency matrix

mergeCloseModules

Merge close modules in gene expression data

consensusProjectiveKMeans

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

normalizeLabels

Transform numerical labels into normal order.

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

kMEcomparisonScatterplot

Function to plot kME values between two comparable data sets.

corPvalueFisher

Fisher's asymptotic p-value for correlation

blockwiseConsensusModules

Find consensus modules across several datasets.

setCorrelationPreservation

Summary correlation preservation measure

relativeCorPredictionSuccess

Compare prediction success

metaAnalysis

Meta-analysis of binary and continuous variables

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

chooseTopHubInEachModule

Chooses the top hub gene in each module

cutreeStaticColor

Constant height tree cut using color labels

spaste

Space-less paste

plotDendroAndColors

Dendrogram plot with color annotation of objects

overlapTableUsingKME

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

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

cutreeStatic

Constant-height tree cut

exportNetworkToVisANT

Export network data in format readable by VisANT

labeledBarplot

Barplot with text or color labels.

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

keepCommonProbes

Keep probes that are shared among given data sets

goodSamples

Filter samples with too many missing entries

Inline display of progress

multiSetMEs

Calculate module eigengenes.

matrixToNetwork

Construct a network from a matrix

projectiveKMeans

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

greenBlackRed

Green-black-red color sequence

colQuantileC

Fast colunm-wise quantile of a matrix.

preservationNetworkConnectivity

Network preservation calculations

displayColors

Show colors used to label modules

labels2colors

Convert numerical labels to colors.

plotColorUnderTree

Plot color rows under a dendrogram

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

intramodularConnectivity

Calculation of intramodular connectivity

sizeGrWindow

Opens a graphics window with specified dimensions

networkScreeningGS

Network gene screening with an external gene significance measure

proportionsInAdmixture

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

signedKME

Signed eigengene-based connectivity

matchLabels

Relabel module labels to best match the given reference labels

mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information

modulePreservation

Calculation of module preservation statistics

overlapTable

Calculate overlap of modules

qvalue

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

plotModuleSignificance

Barplot of module significance

propVarExplained

Proportion of variance explained by eigengenes.

userListEnrichment

Measure enrichment between inputted and user-defined lists

collapseRowsUsingKME

Selects one representative row per group based on kME

subsetTOM

Topological overlap for a subset of a whole set of genes

correlationPreservation

Preservation of eigengene correlations

simulateModule

Simulate a gene co-expression module

simulateDatExpr

Simulation of expression data

moduleMergeUsingKME

Merge modules and reassign genes using kME.

verboseIplot

Scatterplot with density

simulateDatExpr5Modules

Simplified simulation of expression data

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

unsignedAdjacency

Calculation of unsigned adjacency

moduleEigengenes

Calculate module eigengenes.

plotCor

Red and Green Color Image of Correlation Matrix

nearestCentroidPredictor

Nearest centroid predictor

moduleNumber

Fixed-height cut of a dendrogram.

redWhiteGreen

Red-white-green color sequence

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

rankPvalue

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

dynamicMergeCut

Threshold for module merging

simulateEigengeneNetwork

Simulate eigengene network from a causal model

stat.diag.da

Diagonal Discriminant Analysis

vectorTOM

Topological overlap for a subset of the whole set of genes

rgcolors.func

Red and Green Color Specification

stat.bwss

Between and Within Group Sum of Squares Calculation

networkConcepts

Calculations of network concepts

standardColors

Colors this library uses for labeling modules.

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

removePrincipalComponents

Remove leading principal components from data

numbers2colors

Color representation for a numeric variable

stdErr

Standard error of the mean of a given vector.

pquantile

Parallel quantile, median, mean

qvalue.restricted

qvalue convenience wrapper

simulateMultiExpr

Simulate multi-set expression data

networkScreening

Identification of genes related to a trait

randIndex

Rand index of two partitions

labeledHeatmap

Produce a labeled heatmap plot

nPresent

Number of present data entries.

verboseScatterplot

Scatterplot annotated by regression line and p-value

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

plotMEpairs

Pairwise scatterplots of eigengenes

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

votingLinearPredictor

Voting linear predictor

standardScreeningNumericTrait

Standard screening for numeric traits

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

plotNetworkHeatmap

Network heatmap plot

swapTwoBranches

Select, swap, or reflect branches in a dendrogram.

softConnectivity

Calculates connectivity of a weighted network.

orderMEs

Put close eigenvectors next to each other

prepComma

Prepend a comma to a non-empty string

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

stratifiedBarplot

Bar plots of data across two splitting parameters

verboseBarplot

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

plotMat

Red and Green Color Image of Data Matrix

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

signumAdjacencyFunction

Hard-thresholding adjacency function

cor

Fast calculations of Pearson correlation.

goodGenes

Filter genes with too many missing entries

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

nearestNeighborConnectivityMS

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

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

simulateSmallLayer

Simulate small modules

standardScreeningBinaryTrait

Standard screening for binatry traits

scaleFreePlot

Visual check of scale-free topology