⚠️There's a newer version (1.74) of this package.Take me there.

WGCNA (version 0.92-3)

Weighted Gene Co-Expression Network Analysis

Description

Functions necessary to perform Weighted Gene Co-Expression Network Analysis

Copy Link

Version

Install

install.packages('WGCNA')

Monthly Downloads

16,020

Version

0.92-3

License

GPL (>= 2)

Maintainer

Peter Langfelder

Last Published

July 26th, 2010

Functions in WGCNA (0.92-3)

addGrid

Add grid lines to an existing plot.

TOMsimilarityFromExpr

Topological overlap matrix

WGCNA-package

Weighted Gene Co-Expression Network Analysis

greenBlackRed

Green-black-red color sequence

redWhiteGreen

Red-white-green color sequence

automaticNetworkScreening

One-step automatic network gene screening

addGuideLines

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

bicorAndPvalue

Calculation of biweight midcorrelations and associated p-values

networkScreeningGS

Network gene screening with an external gene significance measure

greenWhiteRed

Green-white-red color sequence

corPredictionSuccess

Qunatification of success of gene screening

GOenrichmentAnalysis

Calculation of GO enrichment (experimental)

plot.cor

Red and Green Color Image of Correlation Matrix

cutreeStatic

Constant-height tree cut

goodSamplesGenes

Iterative filtering of samples and genes with too many missing entries

GTOMdist

Generalized Topological Overlap Measure

alignExpr

Align expression data with given vector

labelPoints

Label scatterplot points

conformityBasedNetworkConcepts

Calculation of conformity-based network concepts.

blockwiseModules

Automatic network construction and module detection

goodSamples

Filter samples with too many missing entries

preservationNetworkConnectivity

Network preservation calculations

goodSamplesMS

Filter samples with too many missing entries across multiple data sets

plotDendroAndColors

Dendrogram plot with color annotation of objects

automaticNetworkScreeningGS

One-step automatic network gene screening with external gene significance

checkSets

Check structure and retrieve sizes of a group of datasets.

plotMEpairs

Pairwise scatterplots of eigengenes

fundamentalNetworkConcepts

Calculation of fundamental network concepts from an adjacency matrix.

numbers2colors

Color representation for a numeric variable

goodSamplesGenesMS

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

exportNetworkToVisANT

Export network data in format readable by VisANT

blockwiseConsensusModules

Find consensus modules across several datasets.

vectorTOM

Topological overlap for a subset of the whole set of genes

simulateMultiExpr

Simulate multi-set expression data

simulateSmallLayer

Simulate small modules

colQuantileC

Fast colunm-wise quantile of a matrix.

goodGenes

Filter genes with too many missing entries

metaZfunction

Meta-analysis Z statistic

checkAdjMat

Check adjacency matrix

relativeCorPredictionSuccess

Compare prediction success

multiSetMEs

Calculate module eigengenes.

addTraitToMEs

Add trait information to multi-set module eigengene structure

simulateModule

Simulate a gene co-expression module

modulePreservation

Calculation of module preservation statistics

exportNetworkToCytoscape

Export network to Cytoscape

verboseScatterplot

Scatterplot annotated by regression line and p-value

nearestNeighborConnectivity

Connectivity to a constant number of nearest neighbors

correlationPreservation

Preservation of eigengene correlations

addErrorBars

Add error bars to a barplot.

nPresent

Number of present data entries.

plotEigengeneNetworks

Eigengene network plot

vectorizeMatrix

Turn a matrix into a vector of non-redundant components

subsetTOM

Topological overlap for a subset of a whole set of genes

corAndPvalue

Calculation of correlations and associated p-values

cutreeStaticColor

Constant height tree cut using color labels

cor

Fast calculations of Pearson correlation.

clusterCoef

Clustering coefficient calculation

mergeCloseModules

Merge close modules in gene expression data

displayColors

Show colors used to label modules

sizeGrWindow

Opens a graphics window with specified dimensions

moduleEigengenes

Calculate module eigengenes.

overlapTable

Calculate overlap of modules

plotClusterTreeSamples

Annotated clustering dendrogram of microarray samples

verboseBarplot

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

labels2colors

Convert numerical labels to colors.

verboseBoxplot

Boxplot annotated by a Kruskal-Wallis p-value

hubGeneSignificance

Hubgene significance

simulateDatExpr5Modules

Simplified simulation of expression data

TOMplot

Graphical representation of the Topological Overlap Matrix

matchLabels

Relabel module labels to best match the given reference labels

keepCommonProbes

Keep probes that are shared among given data sets

networkConcepts

Calculations of network concepts

standardColors

Colors this library uses for labeling modules.

removeGreyME

Removes the grey eigengene from a given collection of eigengenes.

stat.bwss

Between and Within Group Sum of Squares Calculation

moduleNumber

Fixed-height cut of a dendrogram.

standardScreeningNumericTrait

Standard screening for numeric traits

consensusProjectiveKMeans

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

rankPvalue

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

pickSoftThreshold

Analysis of scale free topology for soft-thresholding

dynamicMergeCut

Threshold for module merging

corPvalueStudent

Student asymptotic p-value for correlation

plotColorUnderTree

Plot color rows under a dendrogram

labeledHeatmap

Produce a labeled heatmap plot

fixDataStructure

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

orderMEs

Put close eigenvectors next to each other

projectiveKMeans

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

scaleFreePlot

Visual check of scale-free topology

plotNetworkHeatmap

Network heatmap plot

softConnectivity

Calculates connectivity of a weighted network.

normalizeLabels

Transform numerical labels into normal order.

plot.mat

Red and Green Color Image of Data Matrix

labeledBarplot

Barplot with text or color labels.

collapseRows

Collapse Rows in Numeric Matrix

intramodularConnectivity

Calculation of intramodular connectivity

setCorrelationPreservation

Summary correlation preservation measure

simulateEigengeneNetwork

Simulate eigengene network from a causal model

stat.diag.da

Diagonal Discriminant Analysis

standardScreeningCensoredTime

Standard Screening with regard to a Censored Time Variable

recutConsensusTrees

Repeat blockwise consensus module detection from pre-calculated data

randIndex

Rand index of two partitions

collectGarbage

Iterative garbage collection.

rgcolors.func

Red and Green Color Specification

plotModuleSignificance

Barplot of module significance

standardScreeningBinaryTrait

Standard screening for binatry traits

propVarExplained

Proportion of variance explained by eigengenes.

consensusOrderMEs

Put close eigenvectors next to each other in several sets.

scaleFreeFitIndex

Calculation of fitting statistics for evaluating scale free topology fit.

goodGenesMS

Filter genes with too many missing entries across multiple sets

signedKME

Signed eigengene-based connectivity

stdErr

Standard error of the mean of a given vector.

unsignedAdjacency

Calculation of unsigned adjacency

simulateDatExpr

Simulation of expression data

sigmoidAdjacencyFunction

Sigmoid-type adacency function.

pickHardThreshold

Analysis of scale free topology for hard-thresholding.

Inline display of progress

spaste

Space-less paste

signumAdjacencyFunction

Hard-thresholding adjacency function

corPvalueFisher

Fisher's asymptotic p-value for correlation

Basic Statistical Functions for Handling Missing Values

moduleColor.getMEprefix

Get the prefix used to label module eigengenes.

recutBlockwiseTrees

Repeat blockwise module detection from pre-calculated data

bicor

Biweight Midcorrelation

consensusMEDissimilarity

adjacency

Calculate network adjacency

nearestNeighborConnectivityMS

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

networkScreening

Identification of genes related to a trait