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WGCNA (version 1.25-2)
Weighted Correlation Network Analysis
Description
Functions necessary to perform Weighted Correlation Network Analysis
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Install
install.packages('WGCNA')
Monthly Downloads
18,389
Version
1.25-2
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
December 2nd, 2012
Functions in WGCNA (1.25-2)
Search functions
matchLabels
Relabel module labels to best match the given reference labels
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
metaAnalysis
Meta-analysis of binary and continuous variables
colQuantileC
Fast colunm-wise quantile of a matrix.
TrueTrait
Estimate the true trait underlying a list of surrogate markers.
checkAdjMat
Check adjacency matrix
kMEcomparisonScatterplot
Function to plot kME values between two comparable data sets.
coClustering.permutationTest
Permutation test for co-clustering
plotNetworkHeatmap
Network heatmap plot
intramodularConnectivity
Calculation of intramodular connectivity
corPvalueFisher
Fisher's asymptotic p-value for correlation
chooseOneHubInEachModule
Chooses a single hub gene in each module
TOMplot
Graphical representation of the Topological Overlap Matrix
WGCNA-package
Weighted Gene Co-Expression Network Analysis
exportNetworkToCytoscape
Export network to Cytoscape
collapseRowsUsingKME
Selects one representative row per group based on kME
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
goodSamples
Filter samples with too many missing entries
matrixToNetwork
Construct a network from a matrix
plotCor
Red and Green Color Image of Correlation Matrix
blockSize
Attempt to calculate an appropriate block size to maximize efficiency of block-wise calcualtions.
consensusDissTOMandTree
Consensus clustering based on topological overlap and hierarchical clustering
TOMsimilarityFromExpr
Topological overlap matrix
corPredictionSuccess
Qunatification of success of gene screening
displayColors
Show colors used to label modules
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
moduleNumber
Fixed-height cut of a dendrogram.
nPresent
Number of present data entries.
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
clusterCoef
Clustering coefficient calculation
consensusKME
Calculate consensus kME (eigengene-based connectivities) across multiple data sets.
cutreeStatic
Constant-height tree cut
plotDendroAndColors
Dendrogram plot with color annotation of objects
addErrorBars
Add error bars to a barplot.
multiData.eigengeneSignificance
Eigengene significance across multiple sets
fixDataStructure
Put single-set data into a form useful for multiset calculations.
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
SCsLists
Stem Cell-Related Genes with Corresponding Gene Markers
overlapTable
Calculate overlap of modules
moduleEigengenes
Calculate module eigengenes.
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
simulateMultiExpr
Simulate multi-set expression data
collectGarbage
Iterative garbage collection.
exportNetworkToVisANT
Export network data in format readable by VisANT
modulePreservation
Calculation of module preservation statistics
nearestCentroidPredictor
Nearest centroid predictor
networkScreening
Identification of genes related to a trait
BrainLists
Brain-Related Categories with Corresponding Gene Markers
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
greenBlackRed
Green-black-red color sequence
nSets
Number of sets in a multi-set variable
AFcorMI
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
numbers2colors
Color representation for a numeric variable
orderMEs
Put close eigenvectors next to each other
addTraitToMEs
Add trait information to multi-set module eigengene structure
plotEigengeneNetworks
Eigengene network plot
softConnectivity
Calculates connectivity of a weighted network.
alignExpr
Align expression data with given vector
qvalue.restricted
qvalue convenience wrapper
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
chooseTopHubInEachModule
Chooses the top hub gene in each module
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
preservationNetworkConnectivity
Network preservation calculations
standardScreeningBinaryTrait
Standard screening for binatry traits
Inline display of progress
Inline display of progress
corAndPvalue
Calculation of correlations and associated p-values
moduleMergeUsingKME
Merge modules and reassign genes using kME.
relativeCorPredictionSuccess
Compare prediction success
bicor
Biweight Midcorrelation
setCorrelationPreservation
Summary correlation preservation measure
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
allowWGCNAThreads
Allow and disable multi-threading for certain WGCNA calculations
stdErr
Standard error of the mean of a given vector.
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
adjacency.splineReg
Calculate network adjacency based on natural cubic spline regression
redWhiteGreen
Red-white-green color sequence
multiSetMEs
Calculate module eigengenes.
qvalue
Estimate the q-values for a given set of p-values
plotMat
Red and Green Color Image of Data Matrix
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
ImmunePathwayLists
Immune Pathways with Corresponding Gene Markers
sizeGrWindow
Opens a graphics window with specified dimensions
standardScreeningNumericTrait
Standard screening for numeric traits
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
projectiveKMeans
Projective K-means (pre-)clustering of expression data
automaticNetworkScreening
One-step automatic network gene screening
standardColors
Colors this library uses for labeling modules.
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
vectorTOM
Topological overlap for a subset of the whole set of genes
simulateDatExpr
Simulation of expression data
subsetTOM
Topological overlap for a subset of a whole set of genes
verboseScatterplot
Scatterplot annotated by regression line and p-value
coxRegressionResiduals
Deviance- and martingale residuals from a Cox regression model
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
goodGenesMS
Filter genes with too many missing entries across multiple sets
labels2colors
Convert numerical labels to colors.
unsignedAdjacency
Calculation of unsigned adjacency
cor
Fast calculations of Pearson correlation.
stratifiedBarplot
Bar plots of data across two splitting parameters
verboseIplot
Scatterplot with density
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
na
Basic Statistical Functions for Handling Missing Values
networkConcepts
Calculations of network concepts
scaleFreePlot
Visual check of scale-free topology
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
transposeBigData
Transpose a big matrix or data frame
plotMEpairs
Pairwise scatterplots of eigengenes
accuracyMeasures
Accuracy measures for a 2x2 confusion matrix.
addGrid
Add grid lines to an existing plot.
BloodLists
Blood Cell Types with Corresponding Gene Markers
allocateJobs
Divide tasks among workers
votingLinearPredictor
Voting linear predictor
blockwiseModules
Automatic network construction and module detection
plotColorUnderTree
Plot color rows under a dendrogram
prepComma
Prepend a comma to a non-empty string
cutreeStaticColor
Constant height tree cut using color labels
labelPoints
Label scatterplot points
signedKME
Signed eigengene-based connectivity
removePrincipalComponents
Remove leading principal components from data
simulateModule
Simulate a gene co-expression module
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
simulateDatExpr5Modules
Simplified simulation of expression data
blueWhiteRed
Blue-white-red color sequence
coClustering
Co-clustering measure of cluster preservation between two clusterings
keepCommonProbes
Keep probes that are shared among given data sets
dynamicMergeCut
Threshold for module merging
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
proportionsInAdmixture
Estimate the proportion of pure populations in an admixed population based on marker expression values.
correlationPreservation
Preservation of eigengene correlations
mergeCloseModules
Merge close modules in gene expression data
stat.diag.da
Diagonal Discriminant Analysis
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
GTOMdist
Generalized Topological Overlap Measure
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
adjacency.polyReg
Adjacency matrix based on polynomial regression
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
adjacency
Calculate network adjacency
labeledBarplot
Barplot with text or color labels.
networkScreeningGS
Network gene screening with an external gene significance measure
blockwiseIndividualTOMs
Calculation of block-wise topological overlaps
BrainRegionMarkers
Gene Markers for Regions of the Human Brain
blockwiseConsensusModules
Find consensus modules across several datasets.
plotModuleSignificance
Barplot of module significance
normalizeLabels
Transform numerical labels into normal order.
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
rgcolors.func
Red and Green Color Specification
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
overlapTableUsingKME
Determines significant overlap between modules in two networks based on kME tables.
signumAdjacencyFunction
Hard-thresholding adjacency function
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
spaste
Space-less paste
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
pquantile
Parallel quantile, median, mean
stat.bwss
Between and Within Group Sum of Squares Calculation
randIndex
Rand index of two partitions
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
hubGeneSignificance
Hubgene significance
collapseRows
Select one representative row per group
conformityDecomposition
Conformity and module based decomposition of a network adjacency matrix.
goodGenes
Filter genes with too many missing entries
labeledHeatmap
Produce a labeled heatmap plot
propVarExplained
Proportion of variance explained by eigengenes.
simulateEigengeneNetwork
Simulate eigengene network from a causal model
simulateSmallLayer
Simulate small modules
userListEnrichment
Measure enrichment between inputted and user-defined lists
swapTwoBranches
Select, swap, or reflect branches in a dendrogram.
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
checkSets
Check structure and retrieve sizes of a group of datasets.
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
corPvalueStudent
Student asymptotic p-value for correlation
greenWhiteRed
Green-white-red color sequence
lowerTri2matrix
Reconstruct a symmetric matrix from a distance (lower-triangular) representation
metaZfunction
Meta-analysis Z statistic
randomGLMpredictor
Random generalized linear model predictor