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WGCNA (version 0.97)

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

16,020

Version

0.97

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

November 3rd, 2010

Functions in WGCNA (0.97)

bicor

Biweight Midcorrelation

alignExpr

Align expression data with given vector

collapseRows

Select one representative row per group

correlationPreservation

Preservation of eigengene correlations

addGrid

Add grid lines to an existing plot.

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

checkAdjMat

Check adjacency matrix

adjacency

Calculate network adjacency

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

automaticNetworkScreening

One-step automatic network gene screening

WGCNA-package

Weighted Gene Co-Expression Network Analysis

plotModuleSignificance

Barplot of module significance

goodSamplesGenesMS

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

GTOMdist

Generalized Topological Overlap Measure

mergeCloseModules

Merge close modules in gene expression data

addGuideLines

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

relativeCorPredictionSuccess

Compare prediction success

addTraitToMEs

Add trait information to multi-set module eigengene structure

blockwiseModules

Automatic network construction and module detection

corPvalueStudent

Student asymptotic p-value for correlation

TOMplot

Graphical representation of the Topological Overlap Matrix

corPvalueFisher

Fisher's asymptotic p-value for correlation

consensusProjectiveKMeans

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

cutreeStaticColor

Constant height tree cut using color labels

keepCommonProbes

Keep probes that are shared among given data sets

Inline display of progress

greenBlackRed

Green-black-red color sequence

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

intramodularConnectivity

Calculation of intramodular connectivity

standardScreeningBinaryTrait

Standard screening for binatry traits

setCorrelationPreservation

Summary correlation preservation measure

modulePreservation

Calculation of module preservation statistics

consensusMEDissimilarity

Consensus dissimilarity of module eigengenes.

normalizeLabels

Transform numerical labels into normal order.

projectiveKMeans

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

exportNetworkToVisANT

Export network data in format readable by VisANT

nPresent

Number of present data entries.

overlapTable

Calculate overlap of modules

addErrorBars

Add error bars to a barplot.

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

mutualInfoAdjacency

Calculate weighted adjacency matrices based on mutual information

moduleEigengenes

Calculate module eigengenes.

blockwiseConsensusModules

Find consensus modules across several datasets.

goodGenes

Filter genes with too many missing entries

preservationNetworkConnectivity

Network preservation calculations

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

plot.mat

Red and Green Color Image of Data Matrix

sizeGrWindow

Opens a graphics window with specified dimensions

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

plotMEpairs

Pairwise scatterplots of eigengenes

goodSamples

Filter samples with too many missing entries

randIndex

Rand index of two partitions

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

labeledBarplot

Barplot with text or color labels.

clusterCoef

Clustering coefficient calculation

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

nearestNeighborConnectivityMS

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

rgcolors.func

Red and Green Color Specification

rankPvalue

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

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

labelPoints

Label scatterplot points

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

orderMEs

Put close eigenvectors next to each other

greenWhiteRed

Green-white-red color sequence

labels2colors

Convert numerical labels to colors.

simulateDatExpr5Modules

Simplified simulation of expression data

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

collectGarbage

Iterative garbage collection.

exportNetworkToCytoscape

Export network to Cytoscape

TOMsimilarity

Topological overlap matrix similarity and dissimilarity

checkSets

Check structure and retrieve sizes of a group of datasets.

scaleFreePlot

Visual check of scale-free topology

displayColors

Show colors used to label modules

colQuantileC

Fast colunm-wise quantile of a matrix.

fixDataStructure

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

verboseBarplot

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

goodGenesMS

Filter genes with too many missing entries across multiple sets

labeledHeatmap

Produce a labeled heatmap plot

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

dynamicMergeCut

Threshold for module merging

hubGeneSignificance

Hubgene significance

propVarExplained

Proportion of variance explained by eigengenes.

subsetTOM

Topological overlap for a subset of a whole set of genes

stat.bwss

Between and Within Group Sum of Squares Calculation

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

simulateMultiExpr

Simulate multi-set expression data

networkScreeningGS

Network gene screening with an external gene significance measure

simulateEigengeneNetwork

Simulate eigengene network from a causal model

plotColorUnderTree

Plot color rows under a dendrogram

simulateDatExpr

Simulation of expression data

softConnectivity

Calculates connectivity of a weighted network.

Basic Statistical Functions for Handling Missing Values

standardColors

Colors this library uses for labeling modules.

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

multiSetMEs

Calculate module eigengenes.

stdErr

Standard error of the mean of a given vector.

simulateModule

Simulate a gene co-expression module

verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value

simulateSmallLayer

Simulate small modules

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

corAndPvalue

Calculation of correlations and associated p-values

networkConcepts

Calculations of network concepts

plotNetworkHeatmap

Network heatmap plot

matchLabels

Relabel module labels to best match the given reference labels

spaste

Space-less paste

vectorTOM

Topological overlap for a subset of the whole set of genes

signedKME

Signed eigengene-based connectivity

moduleNumber

Fixed-height cut of a dendrogram.

unsignedAdjacency

Calculation of unsigned adjacency

redWhiteGreen

Red-white-green color sequence

networkScreening

Identification of genes related to a trait

stat.diag.da

Diagonal Discriminant Analysis

AUV2predicted

Prediction of Weighted Mutual Information Adjacency Matrix by Correlation

corPredictionSuccess

Qunatification of success of gene screening

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

numbers2colors

Color representation for a numeric variable

standardScreeningNumericTrait

Standard screening for numeric traits

signumAdjacencyFunction

Hard-thresholding adjacency function

plot.cor

Red and Green Color Image of Correlation Matrix

plotEigengeneNetworks

Eigengene network plot

verboseScatterplot

Scatterplot annotated by regression line and p-value

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

TOMsimilarityFromExpr

Topological overlap matrix

cor

Fast calculations of Pearson correlation.

cutreeStatic

Constant-height tree cut

metaZfunction

Meta-analysis Z statistic

plotDendroAndColors

Dendrogram plot with color annotation of objects

pquantile

Parallel quantile, median, mean