⚠️There's a newer version (1.74) of this package.Take me there.

WGCNA (version 1.23-1)

Weighted Correlation Network Analysis

Description

Functions necessary to perform Weighted Correlation Network Analysis

Copy Link

Version

Install

install.packages('WGCNA')

Monthly Downloads

16,020

Version

1.23-1

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

August 3rd, 2012

Functions in WGCNA (1.23-1)

adjacency.polyReg

Adjacency matrix based on polynomial regression

chooseOneHubInEachModule

Chooses a single hub gene in each module

TOMsimilarityFromExpr

Topological overlap matrix

checkAdjMat

Check adjacency matrix

TOMplot

Graphical representation of the Topological Overlap Matrix

checkSets

Check structure and retrieve sizes of a group of datasets.

accuracyMeasures

Accuracy measures for a 2x2 confusion matrix.

consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.

coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model

coClustering

Co-clustering measure of cluster preservation between two clusterings

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

corPredictionSuccess

Qunatification of success of gene screening

allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations

addGrid

Add grid lines to an existing plot.

addErrorBars

Add error bars to a barplot.

goodGenesMS

Filter genes with too many missing entries across multiple sets

labels2colors

Convert numerical labels to colors.

SCsLists

Stem Cell-Related Genes with Corresponding Gene Markers

goodSamplesGenesMS

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

blockwiseConsensusModules

Find consensus modules across several datasets.

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

greenWhiteRed

Green-white-red color sequence

BrainRegionMarkers

Gene Markers for Regions of the Human Brain

BloodLists

Blood Cell Types with Corresponding Gene Markers

cor

Fast calculations of Pearson correlation.

moduleMergeUsingKME

Merge modules and reassign genes using kME.

collapseRowsUsingKME

Selects one representative row per group based on kME

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

orderMEs

Put close eigenvectors next to each other

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

collectGarbage

Iterative garbage collection.

cutreeStaticColor

Constant height tree cut using color labels

dynamicMergeCut

Threshold for module merging

ImmunePathwayLists

Immune Pathways with Corresponding Gene Markers

plotMEpairs

Pairwise scatterplots of eigengenes

moduleEigengenes

Calculate module eigengenes.

correlationPreservation

Preservation of eigengene correlations

TOMsimilarity

Topological overlap matrix similarity and dissimilarity

preservationNetworkConnectivity

Network preservation calculations

prepComma

Prepend a comma to a non-empty string

matrixToNetwork

Construct a network from a matrix

nSets

Number of sets in a multi-set variable

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

corPvalueFisher

Fisher's asymptotic p-value for correlation

collapseRows

Select one representative row per group

GTOMdist

Generalized Topological Overlap Measure

Inline display of progress

WGCNA-package

Weighted Gene Co-Expression Network Analysis

overlapTable

Calculate overlap of modules

blockwiseIndividualTOMs

Calculation of block-wise topological overlaps

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression

automaticNetworkScreening

One-step automatic network gene screening

blueWhiteRed

Blue-white-red color sequence

multiSetMEs

Calculate module eigengenes.

labelPoints

Label scatterplot points

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

proportionsInAdmixture

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

coClustering.permutationTest

Permutation test for co-clustering

clusterCoef

Clustering coefficient calculation

corPvalueStudent

Student asymptotic p-value for correlation

AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation

normalizeLabels

Transform numerical labels into normal order.

kMEcomparisonScatterplot

Function to plot kME values between two comparable data sets.

chooseTopHubInEachModule

Chooses the top hub gene in each module

metaZfunction

Meta-analysis Z statistic

modulePreservation

Calculation of module preservation statistics

plotEigengeneNetworks

Eigengene network plot

metaAnalysis

Meta-analysis of binary and continuous variables

orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.

pquantile

Parallel quantile, median, mean

colQuantileC

Fast colunm-wise quantile of a matrix.

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

plotNetworkHeatmap

Network heatmap plot

cutreeStatic

Constant-height tree cut

greenBlackRed

Green-black-red color sequence

moduleNumber

Fixed-height cut of a dendrogram.

plotDendroAndColors

Dendrogram plot with color annotation of objects

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

relativeCorPredictionSuccess

Compare prediction success

simulateModule

Simulate a gene co-expression module

qvalue.restricted

qvalue convenience wrapper

multiData.eigengeneSignificance

Eigengene significance across multiple sets

networkConcepts

Calculations of network concepts

randIndex

Rand index of two partitions

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

goodGenes

Filter genes with too many missing entries

signumAdjacencyFunction

Hard-thresholding adjacency function

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

Basic Statistical Functions for Handling Missing Values

removePrincipalComponents

Remove leading principal components from data

plotMat

Red and Green Color Image of Data Matrix

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

labeledBarplot

Barplot with text or color labels.

simulateDatExpr5Modules

Simplified simulation of expression data

plotModuleSignificance

Barplot of module significance

populationMeansInAdmixture

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

qvalue

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

BrainLists

Brain-Related Categories with Corresponding Gene Markers

corAndPvalue

Calculation of correlations and associated p-values

propVarExplained

Proportion of variance explained by eigengenes.

scaleFreePlot

Visual check of scale-free topology

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

TrueTrait

Estimate the true trait underlying a list of surrogate markers.

projectiveKMeans

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

fixDataStructure

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

simulateEigengeneNetwork

Simulate eigengene network from a causal model

networkScreening

Identification of genes related to a trait

nearestCentroidPredictor

Nearest centroid predictor

numbers2colors

Color representation for a numeric variable

addTraitToMEs

Add trait information to multi-set module eigengene structure

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

consensusKME

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

labeledHeatmap

Produce a labeled heatmap plot

plotColorUnderTree

Plot color rows under a dendrogram

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

keepCommonProbes

Keep probes that are shared among given data sets

lowerTri2matrix

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

conformityDecomposition

Conformity and module based decomposition of a network adjacency matrix.

addGuideLines

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

consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering

simulateMultiExpr

Simulate multi-set expression data

consensusProjectiveKMeans

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

displayColors

Show colors used to label modules

softConnectivity

Calculates connectivity of a weighted network.

userListEnrichment

Measure enrichment between inputted and user-defined lists

rankPvalue

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

randomGLMpredictor

Random generalized linear model predictor

rgcolors.func

Red and Green Color Specification

vectorTOM

Topological overlap for a subset of the whole set of genes

spaste

Space-less paste

stratifiedBarplot

Bar plots of data across two splitting parameters

nPresent

Number of present data entries.

plotCor

Red and Green Color Image of Correlation Matrix

sizeGrWindow

Opens a graphics window with specified dimensions

redWhiteGreen

Red-white-green color sequence

stat.bwss

Between and Within Group Sum of Squares Calculation

unsignedAdjacency

Calculation of unsigned adjacency

verboseIplot

Scatterplot with density

subsetTOM

Topological overlap for a subset of a whole set of genes

standardColors

Colors this library uses for labeling modules.

verboseBarplot

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

verboseScatterplot

Scatterplot annotated by regression line and p-value

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

alignExpr

Align expression data with given vector

signedKME

Signed eigengene-based connectivity

stat.diag.da

Diagonal Discriminant Analysis

adjacency

Calculate network adjacency

blockwiseModules

Automatic network construction and module detection

exportNetworkToVisANT

Export network data in format readable by VisANT

goodSamples

Filter samples with too many missing entries

stdErr

Standard error of the mean of a given vector.

standardScreeningBinaryTrait

Standard screening for binatry traits

hubGeneSignificance

Hubgene significance

overlapTableUsingKME

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

swapTwoBranches

Select, swap, or reflect branches in a dendrogram.

standardScreeningNumericTrait

Standard screening for numeric traits

votingLinearPredictor

Voting linear predictor

bicor

Biweight Midcorrelation

exportNetworkToCytoscape

Export network to Cytoscape

matchLabels

Relabel module labels to best match the given reference labels

mergeCloseModules

Merge close modules in gene expression data

mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information

networkScreeningGS

Network gene screening with an external gene significance measure

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

setCorrelationPreservation

Summary correlation preservation measure

simulateSmallLayer

Simulate small modules

verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

intramodularConnectivity

Calculation of intramodular connectivity

nearestNeighborConnectivityMS

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

simulateDatExpr

Simulation of expression data