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WGCNA (version 1.25-2)

Weighted Correlation Network Analysis

Description

Functions necessary to perform Weighted Correlation Network Analysis

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Version

Install

install.packages('WGCNA')

Monthly Downloads

11,673

Version

1.25-2

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

December 2nd, 2012

Functions in WGCNA (1.25-2)

matchLabels

Relabel module labels to best match the given reference labels

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

metaAnalysis

Meta-analysis of binary and continuous variables

colQuantileC

Fast colunm-wise quantile of a matrix.

TrueTrait

Estimate the true trait underlying a list of surrogate markers.

checkAdjMat

Check adjacency matrix

kMEcomparisonScatterplot

Function to plot kME values between two comparable data sets.

coClustering.permutationTest

Permutation test for co-clustering

plotNetworkHeatmap

Network heatmap plot

intramodularConnectivity

Calculation of intramodular connectivity

corPvalueFisher

Fisher's asymptotic p-value for correlation

chooseOneHubInEachModule

Chooses a single hub gene in each module

TOMplot

Graphical representation of the Topological Overlap Matrix

WGCNA-package

Weighted Gene Co-Expression Network Analysis

exportNetworkToCytoscape

Export network to Cytoscape

collapseRowsUsingKME

Selects one representative row per group based on kME

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

goodSamples

Filter samples with too many missing entries

matrixToNetwork

Construct a network from a matrix

plotCor

Red and Green Color Image of Correlation Matrix

blockSize

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

consensusDissTOMandTree

Consensus clustering based on topological overlap and hierarchical clustering

TOMsimilarityFromExpr

Topological overlap matrix

corPredictionSuccess

Qunatification of success of gene screening

displayColors

Show colors used to label modules

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

moduleNumber

Fixed-height cut of a dendrogram.

nPresent

Number of present data entries.

consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.

clusterCoef

Clustering coefficient calculation

consensusKME

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

cutreeStatic

Constant-height tree cut

plotDendroAndColors

Dendrogram plot with color annotation of objects

addErrorBars

Add error bars to a barplot.

multiData.eigengeneSignificance

Eigengene significance across multiple sets

fixDataStructure

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

goodSamplesGenesMS

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

SCsLists

Stem Cell-Related Genes with Corresponding Gene Markers

overlapTable

Calculate overlap of modules

moduleEigengenes

Calculate module eigengenes.

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

simulateMultiExpr

Simulate multi-set expression data

collectGarbage

Iterative garbage collection.

exportNetworkToVisANT

Export network data in format readable by VisANT

modulePreservation

Calculation of module preservation statistics

nearestCentroidPredictor

Nearest centroid predictor

networkScreening

Identification of genes related to a trait

BrainLists

Brain-Related Categories with Corresponding Gene Markers

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

greenBlackRed

Green-black-red color sequence

nSets

Number of sets in a multi-set variable

AFcorMI

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation

numbers2colors

Color representation for a numeric variable

orderMEs

Put close eigenvectors next to each other

addTraitToMEs

Add trait information to multi-set module eigengene structure

plotEigengeneNetworks

Eigengene network plot

softConnectivity

Calculates connectivity of a weighted network.

alignExpr

Align expression data with given vector

qvalue.restricted

qvalue convenience wrapper

nearestNeighborConnectivityMS

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

chooseTopHubInEachModule

Chooses the top hub gene in each module

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

preservationNetworkConnectivity

Network preservation calculations

standardScreeningBinaryTrait

Standard screening for binatry traits

Inline display of progress

corAndPvalue

Calculation of correlations and associated p-values

moduleMergeUsingKME

Merge modules and reassign genes using kME.

relativeCorPredictionSuccess

Compare prediction success

bicor

Biweight Midcorrelation

setCorrelationPreservation

Summary correlation preservation measure

populationMeansInAdmixture

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

allowWGCNAThreads

Allow and disable multi-threading for certain WGCNA calculations

stdErr

Standard error of the mean of a given vector.

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

adjacency.splineReg

Calculate network adjacency based on natural cubic spline regression

redWhiteGreen

Red-white-green color sequence

multiSetMEs

Calculate module eigengenes.

qvalue

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

plotMat

Red and Green Color Image of Data Matrix

mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information

ImmunePathwayLists

Immune Pathways with Corresponding Gene Markers

sizeGrWindow

Opens a graphics window with specified dimensions

standardScreeningNumericTrait

Standard screening for numeric traits

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

projectiveKMeans

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

automaticNetworkScreening

One-step automatic network gene screening

standardColors

Colors this library uses for labeling modules.

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

vectorTOM

Topological overlap for a subset of the whole set of genes

simulateDatExpr

Simulation of expression data

subsetTOM

Topological overlap for a subset of a whole set of genes

verboseScatterplot

Scatterplot annotated by regression line and p-value

coxRegressionResiduals

Deviance- and martingale residuals from a Cox regression model

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

goodGenesMS

Filter genes with too many missing entries across multiple sets

labels2colors

Convert numerical labels to colors.

unsignedAdjacency

Calculation of unsigned adjacency

cor

Fast calculations of Pearson correlation.

stratifiedBarplot

Bar plots of data across two splitting parameters

verboseIplot

Scatterplot with density

verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value

Basic Statistical Functions for Handling Missing Values

networkConcepts

Calculations of network concepts

scaleFreePlot

Visual check of scale-free topology

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

transposeBigData

Transpose a big matrix or data frame

plotMEpairs

Pairwise scatterplots of eigengenes

accuracyMeasures

Accuracy measures for a 2x2 confusion matrix.

addGrid

Add grid lines to an existing plot.

BloodLists

Blood Cell Types with Corresponding Gene Markers

allocateJobs

Divide tasks among workers

votingLinearPredictor

Voting linear predictor

blockwiseModules

Automatic network construction and module detection

plotColorUnderTree

Plot color rows under a dendrogram

prepComma

Prepend a comma to a non-empty string

cutreeStaticColor

Constant height tree cut using color labels

labelPoints

Label scatterplot points

signedKME

Signed eigengene-based connectivity

removePrincipalComponents

Remove leading principal components from data

simulateModule

Simulate a gene co-expression module

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

simulateDatExpr5Modules

Simplified simulation of expression data

blueWhiteRed

Blue-white-red color sequence

coClustering

Co-clustering measure of cluster preservation between two clusterings

keepCommonProbes

Keep probes that are shared among given data sets

dynamicMergeCut

Threshold for module merging

TOMsimilarity

Topological overlap matrix similarity and dissimilarity

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

proportionsInAdmixture

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

correlationPreservation

Preservation of eigengene correlations

mergeCloseModules

Merge close modules in gene expression data

stat.diag.da

Diagonal Discriminant Analysis

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

GTOMdist

Generalized Topological Overlap Measure

addGuideLines

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

adjacency.polyReg

Adjacency matrix based on polynomial regression

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

adjacency

Calculate network adjacency

labeledBarplot

Barplot with text or color labels.

networkScreeningGS

Network gene screening with an external gene significance measure

blockwiseIndividualTOMs

Calculation of block-wise topological overlaps

BrainRegionMarkers

Gene Markers for Regions of the Human Brain

blockwiseConsensusModules

Find consensus modules across several datasets.

plotModuleSignificance

Barplot of module significance

normalizeLabels

Transform numerical labels into normal order.

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

rgcolors.func

Red and Green Color Specification

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

overlapTableUsingKME

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

signumAdjacencyFunction

Hard-thresholding adjacency function

consensusProjectiveKMeans

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

spaste

Space-less paste

rankPvalue

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

orderBranchesUsingHubGenes

Optimize dendrogram using branch swaps and reflections.

pquantile

Parallel quantile, median, mean

stat.bwss

Between and Within Group Sum of Squares Calculation

randIndex

Rand index of two partitions

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

hubGeneSignificance

Hubgene significance

collapseRows

Select one representative row per group

conformityDecomposition

Conformity and module based decomposition of a network adjacency matrix.

goodGenes

Filter genes with too many missing entries

labeledHeatmap

Produce a labeled heatmap plot

propVarExplained

Proportion of variance explained by eigengenes.

simulateEigengeneNetwork

Simulate eigengene network from a causal model

simulateSmallLayer

Simulate small modules

userListEnrichment

Measure enrichment between inputted and user-defined lists

swapTwoBranches

Select, swap, or reflect branches in a dendrogram.

verboseBarplot

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

checkSets

Check structure and retrieve sizes of a group of datasets.

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

corPvalueStudent

Student asymptotic p-value for correlation

greenWhiteRed

Green-white-red color sequence

lowerTri2matrix

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

metaZfunction

Meta-analysis Z statistic

randomGLMpredictor

Random generalized linear model predictor