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WGCNA (version 0.93)

Weighted Gene Co-Expression Network Analysis

Description

Functions necessary to perform Weighted Gene Co-Expression Network Analysis

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Version

Install

install.packages('WGCNA')

Monthly Downloads

20,046

Version

0.93

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

August 26th, 2010

Functions in WGCNA (0.93)

greenWhiteRed

Green-white-red color sequence

collapseRows

Collapse Rows in Numeric Matrix

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

networkScreeningGS

Network gene screening with an external gene significance measure

TOMplot

Graphical representation of the Topological Overlap Matrix

AUV2predicted

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation

modulePreservation

Calculation of module preservation statistics

exportNetworkToVisANT

Export network data in format readable by VisANT

corAndPvalue

Calculation of correlations and associated p-values

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

WGCNA-package

Weighted Gene Co-Expression Network Analysis

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

plotColorUnderTree

Plot color rows under a dendrogram

corPvalueStudent

Student asymptotic p-value for correlation

automaticNetworkScreening

One-step automatic network gene screening

clusterCoef

Clustering coefficient calculation

corPredictionSuccess

Qunatification of success of gene screening

addErrorBars

Add error bars to a barplot.

labeledBarplot

Barplot with text or color labels.

goodGenes

Filter genes with too many missing entries

cutreeStaticColor

Constant height tree cut using color labels

addGuideLines

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

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

cor

Fast calculations of Pearson correlation.

propVarExplained

Proportion of variance explained by eigengenes.

metaZfunction

Meta-analysis Z statistic

TOMsimilarity

Topological overlap matrix similarity and dissimilarity

alignExpr

Align expression data with given vector

mergeCloseModules

Merge close modules in gene expression data

adjacency

Calculate network adjacency

GTOMdist

Generalized Topological Overlap Measure

preservationNetworkConnectivity

Network preservation calculations

simulateEigengeneNetwork

Simulate eigengene network from a causal model

blockwiseConsensusModules

Find consensus modules across several datasets.

displayColors

Show colors used to label modules

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

randIndex

Rand index of two partitions

correlationPreservation

Preservation of eigengene correlations

blockwiseModules

Automatic network construction and module detection

networkConcepts

Calculations of network concepts

signumAdjacencyFunction

Hard-thresholding adjacency function

exportNetworkToCytoscape

Export network to Cytoscape

fixDataStructure

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

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

addTraitToMEs

Add trait information to multi-set module eigengene structure

addGrid

Add grid lines to an existing plot.

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

greenBlackRed

Green-black-red color sequence

corPvalueFisher

Fisher's asymptotic p-value for correlation

moduleNumber

Fixed-height cut of a dendrogram.

simulateModule

Simulate a gene co-expression module

nearestNeighborConnectivityMS

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

setCorrelationPreservation

Summary correlation preservation measure

simulateDatExpr5Modules

Simplified simulation of expression data

overlapTable

Calculate overlap of modules

labeledHeatmap

Produce a labeled heatmap plot

relativeCorPredictionSuccess

Compare prediction success

bicor

Biweight Midcorrelation

keepCommonProbes

Keep probes that are shared among given data sets

labels2colors

Convert numerical labels to colors.

Boxplot annotated by a Kruskal-Wallis p-value

stat.bwss

Between and Within Group Sum of Squares Calculation

goodSamples

Filter samples with too many missing entries

simulateSmallLayer

Simulate small modules

verboseBarplot

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

collectGarbage

Iterative garbage collection.

colQuantileC

Fast colunm-wise quantile of a matrix.

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

labelPoints

Label scatterplot points

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

plotDendroAndColors

Dendrogram plot with color annotation of objects

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

signedKME

Signed eigengene-based connectivity

networkScreening

Identification of genes related to a trait

Inline display of progress

plotModuleSignificance

Barplot of module significance

multiSetMEs

Calculate module eigengenes.

rgcolors.func

Red and Green Color Specification

moduleEigengenes

Calculate module eigengenes.

mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information

standardScreeningBinaryTrait

Standard screening for binatry traits

standardScreeningNumericTrait

Standard screening for numeric traits

plot.cor

Red and Green Color Image of Correlation Matrix

plotMEpairs

Pairwise scatterplots of eigengenes

matchLabels

Relabel module labels to best match the given reference labels

redWhiteGreen

Red-white-green color sequence

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

numbers2colors

Color representation for a numeric variable

projectiveKMeans

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

plot.mat

Red and Green Color Image of Data Matrix

sizeGrWindow

Opens a graphics window with specified dimensions

verboseScatterplot

Scatterplot annotated by regression line and p-value

plotEigengeneNetworks

Eigengene network plot

checkSets

Check structure and retrieve sizes of a group of datasets.

dynamicMergeCut

Threshold for module merging

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

spaste

Space-less paste

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

subsetTOM

Topological overlap for a subset of a whole set of genes

orderMEs

Put close eigenvectors next to each other

standardColors

Colors this library uses for labeling modules.

scaleFreePlot

Visual check of scale-free topology

vectorTOM

Topological overlap for a subset of the whole set of genes

stdErr

Standard error of the mean of a given vector.

normalizeLabels

Transform numerical labels into normal order.

simulateDatExpr

Simulation of expression data

Basic Statistical Functions for Handling Missing Values

checkAdjMat

Check adjacency matrix

cutreeStatic

Constant-height tree cut

goodGenesMS

Filter genes with too many missing entries across multiple sets

goodSamplesGenesMS

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

nPresent

Number of present data entries.

softConnectivity

Calculates connectivity of a weighted network.

simulateMultiExpr

Simulate multi-set expression data

rankPvalue

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

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

TOMsimilarityFromExpr

Topological overlap matrix

intramodularConnectivity

Calculation of intramodular connectivity

consensusProjectiveKMeans

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

stat.diag.da

Diagonal Discriminant Analysis

unsignedAdjacency

Calculation of unsigned adjacency