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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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Install
install.packages('WGCNA')
Monthly Downloads
18,389
Version
0.97
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
November 3rd, 2010
Functions in WGCNA (0.97)
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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
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.
na
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