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WGCNA (version 1.34)

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

1.34

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

October 10th, 2013

Functions in WGCNA (1.34)

cutreeStatic

Constant-height tree cut

PWLists

Pathways with Corresponding Gene Markers - Compiled by Mike Palazzolo and Jim Wang from CHDI

labels2colors

Convert numerical labels to colors.

blockwiseIndividualTOMs

Calculation of block-wise topological overlaps

colQuantileC

Fast colunm-wise quantile of a matrix.

allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations

adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression

numbers2colors

Color representation for a numeric variable

blueWhiteRed

Blue-white-red color sequence

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

pquantile

Parallel quantile, median, mean

SCsLists

Stem Cell-Related Genes with Corresponding Gene Markers

AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation

alignExpr

Align expression data with given vector

adjacency

Calculate network adjacency

returnGeneSetsAsList

Return pre-defined gene lists in several biomedical categories.

overlapTable

Calculate overlap of modules

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

conformityDecomposition

Conformity and module based decomposition of a network adjacency matrix.

BrainLists

Brain-Related Categories with Corresponding Gene Markers

proportionsInAdmixture

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

orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.

softConnectivity

Calculates connectivity of a weighted network.

displayColors

Show colors used to label modules

multiSetMEs

Calculate module eigengenes.

mtd.subset

Subset rows and columns in a multiData structure

moduleMergeUsingKME

Merge modules and reassign genes using kME.

orderMEs

Put close eigenvectors next to each other

addTraitToMEs

Add trait information to multi-set module eigengene structure

plotColorUnderTree

Plot color rows in a given order, for example under a dendrogram

blockwiseModules

Automatic network construction and module detection

stat.bwss

Between and Within Group Sum of Squares Calculation

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

branchSplit.dissim

Branch split based on dissimilarity.

networkConcepts

Calculations of network concepts

vectorTOM

Topological overlap for a subset of the whole set of genes

plotMat

Red and Green Color Image of Data Matrix

propVarExplained

Proportion of variance explained by eigengenes.

consensusKME

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

plotMEpairs

Pairwise scatterplots of eigengenes

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

spaste

Space-less paste

redWhiteGreen

Red-white-green color sequence

stdErr

Standard error of the mean of a given vector.

modulePreservation

Calculation of module preservation statistics

addGuideLines

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

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

cor

Fast calculations of Pearson correlation.

simulateEigengeneNetwork

Simulate eigengene network from a causal model

simulateSmallLayer

Simulate small modules

subsetTOM

Topological overlap for a subset of a whole set of genes

goodSamples

Filter samples with too many missing entries

consensusProjectiveKMeans

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

qvalue.restricted

qvalue convenience wrapper

verboseBarplot

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

labeledHeatmap

Produce a labeled heatmap plot

corAndPvalue

Calculation of correlations and associated p-values

projectiveKMeans

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

checkSets

Check structure and retrieve sizes of a group of datasets.

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

BrainRegionMarkers

Gene Markers for Regions of the Human Brain

collapseRowsUsingKME

Selects one representative row per group based on kME

dynamicMergeCut

Threshold for module merging

Basic Statistical Functions for Handling Missing Values

exportNetworkToVisANT

Export network data in format readable by VisANT

keepCommonProbes

Keep probes that are shared among given data sets

addGrid

Add grid lines to an existing plot.

mtd.mapply

Apply a function to elements of given multiData structures.

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

intramodularConnectivity

Calculation of intramodular connectivity

isMultiData

Determine whether the supplied object is a valid multiData structure

TOMplot

Graphical representation of the Topological Overlap Matrix

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

branchEigengeneDissim

Branch dissimilarity based on eigennodes (eigengenes).

chooseTopHubInEachModule

Chooses the top hub gene in each module

blockwiseConsensusModules

Find consensus modules across several datasets.

mergeCloseModules

Merge close modules in gene expression data

rgcolors.func

Red and Green Color Specification

verboseScatterplot

Scatterplot annotated by regression line and p-value

TOMsimilarityFromExpr

Topological overlap matrix

mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information

coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model

moduleNumber

Fixed-height cut of a dendrogram.

rankPvalue

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

ImmunePathwayLists

Immune Pathways with Corresponding Gene Markers

consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.

TOMsimilarity

Topological overlap matrix similarity and dissimilarity

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

checkAdjMat

Check adjacency matrix

transposeBigData

Transpose a big matrix or data frame

WGCNA-package

Weighted Gene Co-Expression Network Analysis

corPredictionSuccess

Qunatification of success of gene screening

list2multiData

Convert a list to a multiData structure and vice-versa.

sizeGrWindow

Opens a graphics window with specified dimensions

cutreeStaticColor

Constant height tree cut using color labels

collectGarbage

Iterative garbage collection.

networkScreening

Identification of genes related to a trait

metaZfunction

Meta-analysis Z statistic

goodGenes

Filter genes with too many missing entries

preservationNetworkConnectivity

Network preservation calculations

standardColors

Colors this library uses for labeling modules.

labelPoints

Label scatterplot points

simulateMultiExpr

Simulate multi-set expression data

adjacency.polyReg

Adjacency matrix based on polynomial regression

TrueTrait

Estimate the true trait underlying a list of surrogate markers.

corPvalueFisher

Fisher's asymptotic p-value for correlation

coClustering.permutationTest

Permutation test for co-clustering

clusterCoef

Clustering coefficient calculation

consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering

hubGeneSignificance

Hubgene significance

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

lowerTri2matrix

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

goodGenesMS

Filter genes with too many missing entries across multiple sets

matchLabels

Relabel module labels to best match the given reference labels

scaleFreePlot

Visual check of scale-free topology

stratifiedBarplot

Bar plots of data across two splitting parameters

goodSamplesGenesMS

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

verboseIplot

Scatterplot with density

votingLinearPredictor

Voting linear predictor

plotNetworkHeatmap

Network heatmap plot

nearestCentroidPredictor

Nearest centroid predictor

metaAnalysis

Meta-analysis of binary and continuous variables

networkScreeningGS

Network gene screening with an external gene significance measure

populationMeansInAdmixture

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

signumAdjacencyFunction

Hard-thresholding adjacency function

fixDataStructure

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

kMEcomparisonScatterplot

Function to plot kME values between two comparable data sets.

swapTwoBranches

Select, swap, or reflect branches in a dendrogram.

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

matrixToNetwork

Construct a network from a matrix

qvalue

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

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

Inline display of progress

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

mtd.simplify

If possible, simplify a multiData structure to a 3-dimensional array.

nSets

Number of sets in a multi-set variable

signedKME

Signed eigengene-based connectivity

standardScreeningNumericTrait

Standard screening for numeric traits

addErrorBars

Add error bars to a barplot.

nearestNeighborConnectivityMS

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

allocateJobs

Divide tasks among workers

accuracyMeasures

Accuracy measures for a 2x2 confusion matrix or for vectors of predicted and observed values.

coClustering

Co-clustering measure of cluster preservation between two clusterings

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

userListEnrichment

Measure enrichment between inputted and user-defined lists

mtd.apply

Apply a function to each set in a multiData structure.

blockSize

Attempt to calculate an appropriate block size to maximize efficiency of block-wise calcualtions.

collapseRows

Select one representative row per group

multiData.eigengeneSignificance

Eigengene significance across multiple sets

plotModuleSignificance

Barplot of module significance

removePrincipalComponents

Remove leading principal components from data

BloodLists

Blood Cell Types with Corresponding Gene Markers

mtd.setColnames

Get and set column names in a multiData structure.

plotEigengeneNetworks

Eigengene network plot

greenWhiteRed

Green-white-red color sequence

plotCor

Red and Green Color Image of Correlation Matrix

nPresent

Number of present data entries.

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

plotDendroAndColors

Dendrogram plot with color annotation of objects

setCorrelationPreservation

Summary correlation preservation measure

stat.diag.da

Diagonal Discriminant Analysis

simulateDatExpr5Modules

Simplified simulation of expression data

relativeCorPredictionSuccess

Compare prediction success

chooseOneHubInEachModule

Chooses a single hub gene in each module

automaticNetworkScreening

One-step automatic network gene screening

corPvalueStudent

Student asymptotic p-value for correlation

mtd.setAttr

Set attributes on each component of a multiData structure

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

randIndex

Rand index of two partitions

standardScreeningBinaryTrait

Standard screening for binatry traits

simulateDatExpr

Simulation of expression data

unsignedAdjacency

Calculation of unsigned adjacency

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

GTOMdist

Generalized Topological Overlap Measure

bicor

Biweight Midcorrelation

moduleEigengenes

Calculate module eigengenes.

greenBlackRed

Green-black-red color sequence

normalizeLabels

Transform numerical labels into normal order.

overlapTableUsingKME

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

verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value

branchSplit

Branch split.

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

correlationPreservation

Preservation of eigengene correlations

exportNetworkToCytoscape

Export network to Cytoscape

labeledBarplot

Barplot with text or color labels.

mtd.rbindSelf

Turn a multiData structure into a single matrix or data frame.

prepComma

Prepend a comma to a non-empty string

simulateModule

Simulate a gene co-expression module