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WGCNA (version 1.41-1)

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

1.41-1

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

June 14th, 2014

Functions in WGCNA (1.41-1)

BrainLists

Brain-Related Categories with Corresponding Gene Markers

adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression

collapseRows

Select one representative row per group

blockwiseConsensusModules

Find consensus modules across several datasets.

preservationNetworkConnectivity

Network preservation calculations

BloodLists

Blood Cell Types with Corresponding Gene Markers

TOMsimilarityFromExpr

Topological overlap matrix

labeledBarplot

Barplot with text or color labels.

networkScreeningGS

Network gene screening with an external gene significance measure

scaleFreePlot

Visual check of scale-free topology

kMEcomparisonScatterplot

Function to plot kME values between two comparable data sets.

corAndPvalue

Calculation of correlations and associated p-values

stratifiedBarplot

Bar plots of data across two splitting parameters

shortenStrings

Shorten given character strings by truncating at a suitable separator.

mtd.apply

Apply a function to each set in a multiData structure.

signedKME

Signed eigengene-based connectivity

userListEnrichment

Measure enrichment between inputted and user-defined lists

networkScreening

Identification of genes related to a trait

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

spaste

Space-less paste

simulateEigengeneNetwork

Simulate eigengene network from a causal model

addErrorBars

Add error bars to a barplot.

greenWhiteRed

Green-white-red color sequence

alignExpr

Align expression data with given vector

vectorTOM

Topological overlap for a subset of the whole set of genes

cor

Fast calculations of Pearson correlation.

blockwiseIndividualTOMs

Calculation of block-wise topological overlaps

adjacency.polyReg

Adjacency matrix based on polynomial regression

lowerTri2matrix

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

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

labels2colors

Convert numerical labels to colors.

mtd.subset

Subset rows and columns in a multiData structure

multiUnion

Union and intersection of multiple sets

coClustering.permutationTest

Permutation test for co-clustering

labelPoints

Label scatterplot points

moduleEigengenes

Calculate module eigengenes.

nPresent

Number of present data entries.

normalizeLabels

Transform numerical labels into normal order.

plotDendroAndColors

Dendrogram plot with color annotation of objects

propVarExplained

Proportion of variance explained by eigengenes.

mtd.rbindSelf

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

plotModuleSignificance

Barplot of module significance

returnGeneSetsAsList

Return pre-defined gene lists in several biomedical categories.

simulateModule

Simulate a gene co-expression module

unsignedAdjacency

Calculation of unsigned adjacency

stat.bwss

Between and Within Group Sum of Squares Calculation

votingLinearPredictor

Voting linear predictor

softConnectivity

Calculates connectivity of a weighted network.

simulateSmallLayer

Simulate small modules

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

WGCNA-package

Weighted Gene Co-Expression Network Analysis

SCsLists

Stem Cell-Related Genes with Corresponding Gene Markers

TOMsimilarity

Topological overlap matrix similarity and dissimilarity

BrainRegionMarkers

Gene Markers for Regions of the Human Brain

addTraitToMEs

Add trait information to multi-set module eigengene structure

addGuideLines

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

blockSize

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

accuracyMeasures

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

checkAdjMat

Check adjacency matrix

multiData.eigengeneSignificance

Eigengene significance across multiple sets

exportNetworkToVisANT

Export network data in format readable by VisANT

overlapTable

Calculate overlap of modules

addGrid

Add grid lines to an existing plot.

Basic Statistical Functions for Handling Missing Values

GTOMdist

Generalized Topological Overlap Measure

cutreeStatic

Constant-height tree cut

consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.

plotColorUnderTree

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

AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation

rankPvalue

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

corPvalueFisher

Fisher's asymptotic p-value for correlation

coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model

correlationPreservation

Preservation of eigengene correlations

TrueTrait

Estimate the true trait underlying a list of surrogate markers.

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

exportNetworkToCytoscape

Export network to Cytoscape

TOMplot

Graphical representation of the Topological Overlap Matrix

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

modulePreservation

Calculation of module preservation statistics

nSets

Number of sets in a multi-set variable

corPredictionSuccess

Qunatification of success of gene screening

qvalue

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

greenBlackRed

Green-black-red color sequence

nearestNeighborConnectivityMS

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

simulateDatExpr

Simulation of expression data

goodSamplesGenesMS

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

metaAnalysis

Meta-analysis of binary and continuous variables

allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations

swapTwoBranches

Select, swap, or reflect branches in a dendrogram.

Inline display of progress

overlapTableUsingKME

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

plotNetworkHeatmap

Network heatmap plot

conformityDecomposition

Conformity and module based decomposition of a network adjacency matrix.

plotEigengeneNetworks

Eigengene network plot

mergeCloseModules

Merge close modules in gene expression data

formatLabels

Break long character strings into multiple lines

chooseTopHubInEachModule

Chooses the top hub gene in each module

projectiveKMeans

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

list2multiData

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

verboseIplot

Scatterplot with density

plotCor

Red and Green Color Image of Correlation Matrix

branchSplit.dissim

Branch split based on dissimilarity.

mtd.simplify

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

randIndex

Rand index of two partitions

collectGarbage

Iterative garbage collection.

consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering

simulateDatExpr5Modules

Simplified simulation of expression data

corPvalueStudent

Student asymptotic p-value for correlation

goodGenesMS

Filter genes with too many missing entries across multiple sets

displayColors

Show colors used to label modules

ImmunePathwayLists

Immune Pathways with Corresponding Gene Markers

networkConcepts

Calculations of network concepts

sizeGrWindow

Opens a graphics window with specified dimensions

adjacency

Calculate network adjacency

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

labeledHeatmap.multiPage

Labeled heatmap divided into several separate plots.

standardColors

Colors this library uses for labeling modules.

blueWhiteRed

Blue-white-red color sequence

branchEigengeneDissim

Branch dissimilarity based on eigennodes (eigengenes).

qvalue.restricted

qvalue convenience wrapper

fixDataStructure

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

colQuantileC

Fast colunm-wise quantile of a matrix.

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

rgcolors.func

Red and Green Color Specification

subsetTOM

Topological overlap for a subset of a whole set of genes

chooseOneHubInEachModule

Chooses a single hub gene in each module

setCorrelationPreservation

Summary correlation preservation measure

goodSamples

Filter samples with too many missing entries

keepCommonProbes

Keep probes that are shared among given data sets

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

matchLabels

Relabel module labels to best match the given reference labels

standardScreeningBinaryTrait

Standard screening for binatry traits

consensusKME

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

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

orderMEs

Put close eigenvectors next to each other

blockwiseModules

Automatic network construction and module detection

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

hubGeneSignificance

Hubgene significance

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

branchSplit

Branch split.

populationMeansInAdmixture

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

relativeCorPredictionSuccess

Compare prediction success

multiData

Create a multiData structure.

consensusProjectiveKMeans

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

signumAdjacencyFunction

Hard-thresholding adjacency function

numbers2colors

Color representation for a numeric variable

simulateMultiExpr

Simulate multi-set expression data

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

stdErr

Standard error of the mean of a given vector.

prepComma

Prepend a comma to a non-empty string

proportionsInAdmixture

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

clusterCoef

Clustering coefficient calculation

removePrincipalComponents

Remove leading principal components from data

intramodularConnectivity

Calculation of intramodular connectivity

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

automaticNetworkScreening

One-step automatic network gene screening

standardScreeningNumericTrait

Standard screening for numeric traits

dynamicMergeCut

Threshold for module merging

mtd.setColnames

Get and set column names in a multiData structure.

verboseBarplot

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

plotMat

Red and Green Color Image of Data Matrix

goodGenes

Filter genes with too many missing entries

multiSetMEs

Calculate module eigengenes.

allocateJobs

Divide tasks among workers

stat.diag.da

Diagonal Discriminant Analysis

verboseScatterplot

Scatterplot annotated by regression line and p-value

moduleNumber

Fixed-height cut of a dendrogram.

bicor

Biweight Midcorrelation

labeledHeatmap

Produce a labeled heatmap plot

mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

checkSets

Check structure and retrieve sizes of a group of datasets.

coClustering

Co-clustering measure of cluster preservation between two clusterings

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

matrixToNetwork

Construct a network from a matrix

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

transposeBigData

Transpose a big matrix or data frame

metaZfunction

Meta-analysis Z statistic

prependZeros

Pad numbers with leading zeros to specified total width

plotMEpairs

Pairwise scatterplots of eigengenes

mtd.setAttr

Set attributes on each component of a multiData structure

PWLists

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

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

cutreeStaticColor

Constant height tree cut using color labels

moduleMergeUsingKME

Merge modules and reassign genes using kME.

orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

collapseRowsUsingKME

Selects one representative row per group based on kME

mtd.mapply

Apply a function to elements of given multiData structures.

isMultiData

Determine whether the supplied object is a valid multiData structure

nearestCentroidPredictor

Nearest centroid predictor

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

pquantile

Parallel quantile, median, mean

verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value

redWhiteGreen

Red-white-green color sequence