RDocumentation
Moon
Learn R
Search all packages and functions
⚠️
There's a newer version (1.72-5) of this package.
Take me there.
WGCNA (version 1.10-2)
Weighted Gene Co-Expression Network Analysis
Description
Functions necessary to perform Weighted Gene Co-Expression Network Analysis
Copy Link
Copy
Link to current version
Version
Version
1.72-5
1.72-1
1.71
1.70-3
1.69
1.68
1.67
1.66
1.64-1
1.63
1.62
1.61
1.60
1.51
1.49
1.48
1.47
1.46
1.43
1.42
1.41-1
1.34
1.27-1
1.26
1.25-2
1.25-1
1.23-1
1.22
1.20
1.19
1.18-2
1.18-1
1.17
1.15
1.14
1.13
1.12
1.11-3
1.11-2
1.11-1
1.10-2
1.00
0.99
0.98
0.97
0.96
0.95
0.94
0.93
0.92-3
Down Chevron
Install
install.packages('WGCNA')
Monthly Downloads
18,389
Version
1.10-2
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
April 24th, 2011
Functions in WGCNA (1.10-2)
Search functions
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
TOMsimilarityFromExpr
Topological overlap matrix
pquantile
Parallel quantile, median, mean
blockwiseModules
Automatic network construction and module detection
alignExpr
Align expression data with given vector
automaticNetworkScreening
One-step automatic network gene screening
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
addTraitToMEs
Add trait information to multi-set module eigengene structure
networkConcepts
Calculations of network concepts
scaleFreePlot
Visual check of scale-free topology
dynamicMergeCut
Threshold for module merging
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
cor
Fast calculations of Pearson correlation.
BrainLists
Brain-Related Categories with Corresponding Gene Markers
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
Inline display of progress
Inline display of progress
blockwiseConsensusModules
Find consensus modules across several datasets.
matchLabels
Relabel module labels to best match the given reference labels
bicor
Biweight Midcorrelation
labeledBarplot
Barplot with text or color labels.
goodSamples
Filter samples with too many missing entries
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
adjacency.polyReg
Adjacency matrix based on polynomial regression
moduleNumber
Fixed-height cut of a dendrogram.
GTOMdist
Generalized Topological Overlap Measure
stratifiedBarplot
Bar plots of data across two splitting parameters
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
corPvalueFisher
Fisher's asymptotic p-value for correlation
subsetTOM
Topological overlap for a subset of a whole set of genes
checkAdjMat
Check adjacency matrix
preservationNetworkConnectivity
Network preservation calculations
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix.
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
hubGeneSignificance
Hubgene significance
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
multiSetMEs
Calculate module eigengenes.
conformityDecomposition
Conformity vector(s) and factorizability measure(s) of a network
moduleMergeUsingKME
Merge modules and reassign genes using kME.
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
goodGenesMS
Filter genes with too many missing entries across multiple sets
fixDataStructure
Put single-set data into a form useful for multiset calculations.
plotModuleSignificance
Barplot of module significance
exportNetworkToCytoscape
Export network to Cytoscape
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
numbers2colors
Color representation for a numeric variable
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
networkScreening
Identification of genes related to a trait
networkScreeningGS
Network gene screening with an external gene significance measure
plotColorUnderTree
Plot color rows under a dendrogram
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
coClustering
Co-clustering measure of cluster preservation between two clusterings
mergeCloseModules
Merge close modules in gene expression data
cutreeStaticColor
Constant height tree cut using color labels
modulePreservation
Calculation of module preservation statistics
corAndPvalue
Calculation of correlations and associated p-values
matrixToNetwork
Construct a network from a matrix
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
addErrorBars
Add error bars to a barplot.
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
exportNetworkToVisANT
Export network data in format readable by VisANT
chooseTopHubInEachModule
Chooses the top hub gene in each module
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
plotNetworkHeatmap
Network heatmap plot
simulateEigengeneNetwork
Simulate eigengene network from a causal model
WGCNA-package
Weighted Gene Co-Expression Network Analysis
standardScreeningNumericTrait
Standard screening for numeric traits
stat.diag.da
Diagonal Discriminant Analysis
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
rgcolors.func
Red and Green Color Specification
cutreeStatic
Constant-height tree cut
simulateSmallLayer
Simulate small modules
sizeGrWindow
Opens a graphics window with specified dimensions
simulateDatExpr5Modules
Simplified simulation of expression data
clusterCoef
Clustering coefficient calculation
collectGarbage
Iterative garbage collection.
standardColors
Colors this library uses for labeling modules.
simulateDatExpr
Simulation of expression data
collapseRows
Select one representative row per group
addGrid
Add grid lines to an existing plot.
coClustering.permutationTest
Permutation test for co-clustering
plotMEpairs
Pairwise scatterplots of eigengenes
displayColors
Show colors used to label modules
checkSets
Check structure and retrieve sizes of a group of datasets.
qvalue
Estimate the q-values for a given set of p-values
collapseRowsUsingKME
Selects one representative row per group based on kME
redWhiteGreen
Red-white-green color sequence
metaZfunction
Meta-analysis Z statistic
goodGenes
Filter genes with too many missing entries
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
labelPoints
Label scatterplot points
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
corPvalueStudent
Student asymptotic p-value for correlation
BloodLists
Blood Cell Types with Corresponding Gene Markers
moduleEigengenes
Calculate module eigengenes.
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
greenWhiteRed
Green-white-red color sequence
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
normalizeLabels
Transform numerical labels into normal order.
adjacency
Calculate network adjacency
labels2colors
Convert numerical labels to colors.
colQuantileC
Fast colunm-wise quantile of a matrix.
na
Basic Statistical Functions for Handling Missing Values
correlationPreservation
Preservation of eigengene correlations
nPresent
Number of present data entries.
plotEigengeneNetworks
Eigengene network plot
greenBlackRed
Green-black-red color sequence
corPredictionSuccess
Qunatification of success of gene screening
setCorrelationPreservation
Summary correlation preservation measure
keepCommonProbes
Keep probes that are shared among given data sets
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
prepComma
Prepend a comma to a non-empty string
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
labeledHeatmap
Produce a labeled heatmap plot
relativeCorPredictionSuccess
Compare prediction success
spaste
Space-less paste
overlapTable
Calculate overlap of modules
chooseOneHubInEachModule
Chooses a single hub gene in each module
stdErr
Standard error of the mean of a given vector.
randIndex
Rand index of two partitions
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
unsignedAdjacency
Calculation of unsigned adjacency
stat.bwss
Between and Within Group Sum of Squares Calculation
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
signedKME
Signed eigengene-based connectivity
userListEnrichment
Measure enrichment between inputted and user-defined lists
simulateMultiExpr
Simulate multi-set expression data
nearestCentroidPredictor
Nearest centroid predictor
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
projectiveKMeans
Projective K-means (pre-)clustering of expression data
verboseScatterplot
Scatterplot annotated by regression line and p-value
removePrincipalComponents
Remove leading principal components from data
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
plot.cor
Red and Green Color Image of Correlation Matrix
propVarExplained
Proportion of variance explained by eigengenes.
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
plot.mat
Red and Green Color Image of Data Matrix
plotDendroAndColors
Dendrogram plot with color annotation of objects
votingLinearPredictor
Voting linear predictor
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
simulateModule
Simulate a gene co-expression module
vectorTOM
Topological overlap for a subset of the whole set of genes
signumAdjacencyFunction
Hard-thresholding adjacency function
softConnectivity
Calculates connectivity of a weighted network.
TOMplot
Graphical representation of the Topological Overlap Matrix
intramodularConnectivity
Calculation of intramodular connectivity
orderMEs
Put close eigenvectors next to each other
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
standardScreeningBinaryTrait
Standard screening for binatry traits
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value