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 1.23-1)
Weighted Correlation Network Analysis
Description
Functions necessary to perform Weighted Correlation 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
1.23-1
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
August 3rd, 2012
Functions in WGCNA (1.23-1)
Search functions
adjacency.polyReg
Adjacency matrix based on polynomial regression
chooseOneHubInEachModule
Chooses a single hub gene in each module
TOMsimilarityFromExpr
Topological overlap matrix
checkAdjMat
Check adjacency matrix
TOMplot
Graphical representation of the Topological Overlap Matrix
checkSets
Check structure and retrieve sizes of a group of datasets.
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix.
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
coClustering
Co-clustering measure of cluster preservation between two clusterings
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
corPredictionSuccess
Qunatification of success of gene screening
allowWGCNAThreads
Allow and disable multi-threading for certain WGCNA calculations
addGrid
Add grid lines to an existing plot.
addErrorBars
Add error bars to a barplot.
goodGenesMS
Filter genes with too many missing entries across multiple sets
labels2colors
Convert numerical labels to colors.
SCsLists
Stem Cell-Related Genes with Corresponding Gene Markers
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
blockwiseConsensusModules
Find consensus modules across several datasets.
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
greenWhiteRed
Green-white-red color sequence
BrainRegionMarkers
Gene Markers for Regions of the Human Brain
BloodLists
Blood Cell Types with Corresponding Gene Markers
cor
Fast calculations of Pearson correlation.
moduleMergeUsingKME
Merge modules and reassign genes using kME.
collapseRowsUsingKME
Selects one representative row per group based on kME
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
orderMEs
Put close eigenvectors next to each other
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
collectGarbage
Iterative garbage collection.
cutreeStaticColor
Constant height tree cut using color labels
dynamicMergeCut
Threshold for module merging
ImmunePathwayLists
Immune Pathways with Corresponding Gene Markers
plotMEpairs
Pairwise scatterplots of eigengenes
moduleEigengenes
Calculate module eigengenes.
correlationPreservation
Preservation of eigengene correlations
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
preservationNetworkConnectivity
Network preservation calculations
prepComma
Prepend a comma to a non-empty string
matrixToNetwork
Construct a network from a matrix
nSets
Number of sets in a multi-set variable
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
corPvalueFisher
Fisher's asymptotic p-value for correlation
collapseRows
Select one representative row per group
GTOMdist
Generalized Topological Overlap Measure
Inline display of progress
Inline display of progress
WGCNA-package
Weighted Gene Co-Expression Network Analysis
overlapTable
Calculate overlap of modules
blockwiseIndividualTOMs
Calculation of block-wise topological overlaps
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
automaticNetworkScreening
One-step automatic network gene screening
blueWhiteRed
Blue-white-red color sequence
multiSetMEs
Calculate module eigengenes.
labelPoints
Label scatterplot points
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
coClustering.permutationTest
Permutation test for co-clustering
clusterCoef
Clustering coefficient calculation
corPvalueStudent
Student asymptotic p-value for correlation
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
normalizeLabels
Transform numerical labels into normal order.
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
chooseTopHubInEachModule
Chooses the top hub gene in each module
metaZfunction
Meta-analysis Z statistic
modulePreservation
Calculation of module preservation statistics
plotEigengeneNetworks
Eigengene network plot
metaAnalysis
Meta-analysis of binary and continuous variables
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
pquantile
Parallel quantile, median, mean
colQuantileC
Fast colunm-wise quantile of a matrix.
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
plotNetworkHeatmap
Network heatmap plot
cutreeStatic
Constant-height tree cut
greenBlackRed
Green-black-red color sequence
moduleNumber
Fixed-height cut of a dendrogram.
plotDendroAndColors
Dendrogram plot with color annotation of objects
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
relativeCorPredictionSuccess
Compare prediction success
simulateModule
Simulate a gene co-expression module
qvalue.restricted
qvalue convenience wrapper
multiData.eigengeneSignificance
Eigengene significance across multiple sets
networkConcepts
Calculations of network concepts
randIndex
Rand index of two partitions
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
goodGenes
Filter genes with too many missing entries
signumAdjacencyFunction
Hard-thresholding adjacency function
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
na
Basic Statistical Functions for Handling Missing Values
removePrincipalComponents
Remove leading principal components from data
plotMat
Red and Green Color Image of Data Matrix
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
labeledBarplot
Barplot with text or color labels.
simulateDatExpr5Modules
Simplified simulation of expression data
plotModuleSignificance
Barplot of module significance
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
qvalue
Estimate the q-values for a given set of p-values
BrainLists
Brain-Related Categories with Corresponding Gene Markers
corAndPvalue
Calculation of correlations and associated p-values
propVarExplained
Proportion of variance explained by eigengenes.
scaleFreePlot
Visual check of scale-free topology
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
TrueTrait
Estimate the true trait underlying a list of surrogate markers.
projectiveKMeans
Projective K-means (pre-)clustering of expression data
fixDataStructure
Put single-set data into a form useful for multiset calculations.
simulateEigengeneNetwork
Simulate eigengene network from a causal model
networkScreening
Identification of genes related to a trait
nearestCentroidPredictor
Nearest centroid predictor
numbers2colors
Color representation for a numeric variable
addTraitToMEs
Add trait information to multi-set module eigengene structure
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
consensusKME
Calculate consensus kME (eigengene-based connectivities) across multiple data sets.
labeledHeatmap
Produce a labeled heatmap plot
plotColorUnderTree
Plot color rows under a dendrogram
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
keepCommonProbes
Keep probes that are shared among given data sets
lowerTri2matrix
Reconstruct a symmetric matrix from a distance (lower-triangular) representation
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
simulateMultiExpr
Simulate multi-set expression data
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
displayColors
Show colors used to label modules
softConnectivity
Calculates connectivity of a weighted network.
userListEnrichment
Measure enrichment between inputted and user-defined lists
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
randomGLMpredictor
Random generalized linear model predictor
rgcolors.func
Red and Green Color Specification
vectorTOM
Topological overlap for a subset of the whole set of genes
spaste
Space-less paste
stratifiedBarplot
Bar plots of data across two splitting parameters
nPresent
Number of present data entries.
plotCor
Red and Green Color Image of Correlation Matrix
sizeGrWindow
Opens a graphics window with specified dimensions
redWhiteGreen
Red-white-green color sequence
stat.bwss
Between and Within Group Sum of Squares Calculation
unsignedAdjacency
Calculation of unsigned adjacency
verboseIplot
Scatterplot with density
subsetTOM
Topological overlap for a subset of a whole set of genes
standardColors
Colors this library uses for labeling modules.
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
verboseScatterplot
Scatterplot annotated by regression line and p-value
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
alignExpr
Align expression data with given vector
signedKME
Signed eigengene-based connectivity
stat.diag.da
Diagonal Discriminant Analysis
adjacency
Calculate network adjacency
blockwiseModules
Automatic network construction and module detection
exportNetworkToVisANT
Export network data in format readable by VisANT
goodSamples
Filter samples with too many missing entries
stdErr
Standard error of the mean of a given vector.
standardScreeningBinaryTrait
Standard screening for binatry traits
hubGeneSignificance
Hubgene significance
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
standardScreeningNumericTrait
Standard screening for numeric traits
votingLinearPredictor
Voting linear predictor
bicor
Biweight Midcorrelation
exportNetworkToCytoscape
Export network to Cytoscape
matchLabels
Relabel module labels to best match the given reference labels
mergeCloseModules
Merge close modules in gene expression data
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
networkScreeningGS
Network gene screening with an external gene significance measure
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
setCorrelationPreservation
Summary correlation preservation measure
simulateSmallLayer
Simulate small modules
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
intramodularConnectivity
Calculation of intramodular connectivity
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
simulateDatExpr
Simulation of expression data