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WGCNA (version 1.19)

Weighted Correlation Network Analysis

Description

Functions necessary to perform Weighted Correlation Network Analysis

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Version

Install

install.packages('WGCNA')

Monthly Downloads

20,046

Version

1.19

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

March 3rd, 2012

Functions in WGCNA (1.19)

collapseRowsUsingKME

Selects one representative row per group based on kME

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

corPredictionSuccess

Qunatification of success of gene screening

GTOMdist

Generalized Topological Overlap Measure

cutreeStaticColor

Constant height tree cut using color labels

AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation

consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.

addTraitToMEs

Add trait information to multi-set module eigengene structure

colQuantileC

Fast colunm-wise quantile of a matrix.

addErrorBars

Add error bars to a barplot.

coClustering.permutationTest

Permutation test for co-clustering

chooseTopHubInEachModule

Chooses the top hub gene in each module

coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model

populationMeansInAdmixture

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

goodSamples

Filter samples with too many missing entries

dynamicMergeCut

Threshold for module merging

matchLabels

Relabel module labels to best match the given reference labels

kMEcomparisonScatterplot

Function to plot kME values between two comparable data sets.

adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression

overlapTableUsingKME

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

collapseRows

Select one representative row per group

checkSets

Check structure and retrieve sizes of a group of datasets.

automaticNetworkScreening

One-step automatic network gene screening

corPvalueFisher

Fisher's asymptotic p-value for correlation

consensusKME

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

cor

Fast calculations of Pearson correlation.

numbers2colors

Color representation for a numeric variable

moduleNumber

Fixed-height cut of a dendrogram.

correlationPreservation

Preservation of eigengene correlations

propVarExplained

Proportion of variance explained by eigengenes.

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering

addGrid

Add grid lines to an existing plot.

goodSamplesGenesMS

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

corPvalueStudent

Student asymptotic p-value for correlation

chooseOneHubInEachModule

Chooses a single hub gene in each module

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

TOMplot

Graphical representation of the Topological Overlap Matrix

TOMsimilarity

Topological overlap matrix similarity and dissimilarity

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

labeledBarplot

Barplot with text or color labels.

projectiveKMeans

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

Inline display of progress

clusterCoef

Clustering coefficient calculation

labeledHeatmap

Produce a labeled heatmap plot

blockwiseConsensusModules

Find consensus modules across several datasets.

SCsLists

Stem Cell-Related Genes with Corresponding Gene Markers

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

rankPvalue

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

exportNetworkToCytoscape

Export network to Cytoscape

keepCommonProbes

Keep probes that are shared among given data sets

networkScreening

Identification of genes related to a trait

stratifiedBarplot

Bar plots of data across two splitting parameters

plotDendroAndColors

Dendrogram plot with color annotation of objects

corAndPvalue

Calculation of correlations and associated p-values

labelPoints

Label scatterplot points

lowerTri2matrix

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

pquantile

Parallel quantile, median, mean

labels2colors

Convert numerical labels to colors.

plotNetworkHeatmap

Network heatmap plot

mergeCloseModules

Merge close modules in gene expression data

plotColorUnderTree

Plot color rows under a dendrogram

moduleMergeUsingKME

Merge modules and reassign genes using kME.

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

coClustering

Co-clustering measure of cluster preservation between two clusterings

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

TrueTrait

Estimate the true trait underlying a list of surrogate markers.

conformityDecomposition

Conformity and module based decomposition of a network adjacency matrix.

TOMsimilarityFromExpr

Topological overlap matrix

adjacency

Calculate network adjacency

relativeCorPredictionSuccess

Compare prediction success

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

nearestCentroidPredictor

Nearest centroid predictor

matrixToNetwork

Construct a network from a matrix

nPresent

Number of present data entries.

allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

adjacency.polyReg

Adjacency matrix based on polynomial regression

verboseBarplot

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

consensusProjectiveKMeans

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

networkConcepts

Calculations of network concepts

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

randIndex

Rand index of two partitions

bicor

Biweight Midcorrelation

accuracyMeasures

Accuracy measures for a 2x2 confusion matrix.

scaleFreePlot

Visual check of scale-free topology

greenBlackRed

Green-black-red color sequence

WGCNA-package

Weighted Gene Co-Expression Network Analysis

vectorTOM

Topological overlap for a subset of the whole set of genes

overlapTable

Calculate overlap of modules

exportNetworkToVisANT

Export network data in format readable by VisANT

cutreeStatic

Constant-height tree cut

standardScreeningNumericTrait

Standard screening for numeric traits

goodGenes

Filter genes with too many missing entries

moduleEigengenes

Calculate module eigengenes.

greenWhiteRed

Green-white-red color sequence

fixDataStructure

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

hubGeneSignificance

Hubgene significance

metaAnalysis

Meta-analysis of binary and continuous variables

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

blockwiseIndividualTOMs

Calculation of block-wise topological overlaps

checkAdjMat

Check adjacency matrix

displayColors

Show colors used to label modules

addGuideLines

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

plotEigengeneNetworks

Eigengene network plot

simulateModule

Simulate a gene co-expression module

multiSetMEs

Calculate module eigengenes.

simulateSmallLayer

Simulate small modules

rgcolors.func

Red and Green Color Specification

modulePreservation

Calculation of module preservation statistics

swapTwoBranches

Select, swap, or reflect branches in a dendrogram.

userListEnrichment

Measure enrichment between inputted and user-defined lists

prepComma

Prepend a comma to a non-empty string

mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information

redWhiteGreen

Red-white-green color sequence

stdErr

Standard error of the mean of a given vector.

verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value

Basic Statistical Functions for Handling Missing Values

goodGenesMS

Filter genes with too many missing entries across multiple sets

intramodularConnectivity

Calculation of intramodular connectivity

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

alignExpr

Align expression data with given vector

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

qvalue.restricted

qvalue convenience wrapper

sizeGrWindow

Opens a graphics window with specified dimensions

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

standardScreeningBinaryTrait

Standard screening for binatry traits

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

unsignedAdjacency

Calculation of unsigned adjacency

metaZfunction

Meta-analysis Z statistic

simulateEigengeneNetwork

Simulate eigengene network from a causal model

votingLinearPredictor

Voting linear predictor

plotCor

Red and Green Color Image of Correlation Matrix

setCorrelationPreservation

Summary correlation preservation measure

plotMat

Red and Green Color Image of Data Matrix

nearestNeighborConnectivityMS

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

signumAdjacencyFunction

Hard-thresholding adjacency function

networkScreeningGS

Network gene screening with an external gene significance measure

verboseIplot

Scatterplot with density

plotMEpairs

Pairwise scatterplots of eigengenes

simulateDatExpr5Modules

Simplified simulation of expression data

signedKME

Signed eigengene-based connectivity

plotModuleSignificance

Barplot of module significance

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

softConnectivity

Calculates connectivity of a weighted network.

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

preservationNetworkConnectivity

Network preservation calculations

removePrincipalComponents

Remove leading principal components from data

proportionsInAdmixture

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

verboseScatterplot

Scatterplot annotated by regression line and p-value

normalizeLabels

Transform numerical labels into normal order.

nSets

Number of sets in a multi-set variable

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

orderMEs

Put close eigenvectors next to each other

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

spaste

Space-less paste

blockwiseModules

Automatic network construction and module detection

qvalue

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

simulateMultiExpr

Simulate multi-set expression data

standardColors

Colors this library uses for labeling modules.

multiData.eigengeneSignificance

Eigengene significance across multiple sets

simulateDatExpr

Simulation of expression data

stat.diag.da

Diagonal Discriminant Analysis

stat.bwss

Between and Within Group Sum of Squares Calculation

subsetTOM

Topological overlap for a subset of a whole set of genes

BloodLists

Blood Cell Types with Corresponding Gene Markers

BrainLists

Brain-Related Categories with Corresponding Gene Markers

collectGarbage

Iterative garbage collection.

orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.