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WGCNA (version 1.00)
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
1.00
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
February 15th, 2011
Functions in WGCNA (1.00)
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sigmoidAdjacencyFunction
Sigmoid-type adacency function.
orderMEs
Put close eigenvectors next to each other
GTOMdist
Generalized Topological Overlap Measure
alignExpr
Align expression data with given vector
cutreeStaticColor
Constant height tree cut using color labels
bicor
Biweight Midcorrelation
greenWhiteRed
Green-white-red color sequence
simulateModule
Simulate a gene co-expression module
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
labeledBarplot
Barplot with text or color labels.
colQuantileC
Fast colunm-wise quantile of a matrix.
addErrorBars
Add error bars to a barplot.
corAndPvalue
Calculation of correlations and associated p-values
TOMsimilarityFromExpr
Topological overlap matrix
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
corPvalueStudent
Student asymptotic p-value for correlation
multiSetMEs
Calculate module eigengenes.
addGrid
Add grid lines to an existing plot.
relativeCorPredictionSuccess
Compare prediction success
labeledHeatmap
Produce a labeled heatmap plot
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
networkConcepts
Calculations of network concepts
unsignedAdjacency
Calculation of unsigned adjacency
blockwiseConsensusModules
Find consensus modules across several datasets.
moduleNumber
Fixed-height cut of a dendrogram.
propVarExplained
Proportion of variance explained by eigengenes.
plotEigengeneNetworks
Eigengene network plot
signumAdjacencyFunction
Hard-thresholding adjacency function
automaticNetworkScreening
One-step automatic network gene screening
collapseRows
Select one representative row per group
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
prepComma
Prepend a comma to a non-empty string
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
addTraitToMEs
Add trait information to multi-set module eigengene structure
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
subsetTOM
Topological overlap for a subset of a whole set of genes
TOMplot
Graphical representation of the Topological Overlap Matrix
dynamicMergeCut
Threshold for module merging
standardScreeningBinaryTrait
Standard screening for binatry traits
blockwiseModules
Automatic network construction and module detection
plotDendroAndColors
Dendrogram plot with color annotation of objects
mergeCloseModules
Merge close modules in gene expression data
simulateMultiExpr
Simulate multi-set expression data
stat.bwss
Between and Within Group Sum of Squares Calculation
exportNetworkToCytoscape
Export network to Cytoscape
nPresent
Number of present data entries.
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
intramodularConnectivity
Calculation of intramodular connectivity
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
goodGenesMS
Filter genes with too many missing entries across multiple sets
overlapTable
Calculate overlap of modules
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
checkSets
Check structure and retrieve sizes of a group of datasets.
cutreeStatic
Constant-height tree cut
goodGenes
Filter genes with too many missing entries
numbers2colors
Color representation for a numeric variable
plotNetworkHeatmap
Network heatmap plot
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
standardScreeningNumericTrait
Standard screening for numeric traits
keepCommonProbes
Keep probes that are shared among given data sets
sizeGrWindow
Opens a graphics window with specified dimensions
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
pquantile
Parallel quantile, median, mean
greenBlackRed
Green-black-red color sequence
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
exportNetworkToVisANT
Export network data in format readable by VisANT
spaste
Space-less paste
hubGeneSignificance
Hubgene significance
corPredictionSuccess
Qunatification of success of gene screening
projectiveKMeans
Projective K-means (pre-)clustering of expression data
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
corPvalueFisher
Fisher's asymptotic p-value for correlation
correlationPreservation
Preservation of eigengene correlations
displayColors
Show colors used to label modules
Inline display of progress
Inline display of progress
goodSamples
Filter samples with too many missing entries
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
randIndex
Rand index of two partitions
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
modulePreservation
Calculation of module preservation statistics
WGCNA-package
Weighted Gene Co-Expression Network Analysis
matchLabels
Relabel module labels to best match the given reference labels
stat.diag.da
Diagonal Discriminant Analysis
preservationNetworkConnectivity
Network preservation calculations
plotMEpairs
Pairwise scatterplots of eigengenes
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
normalizeLabels
Transform numerical labels into normal order.
na
Basic Statistical Functions for Handling Missing Values
simulateDatExpr
Simulation of expression data
networkScreeningGS
Network gene screening with an external gene significance measure
plot.cor
Red and Green Color Image of Correlation Matrix
labels2colors
Convert numerical labels to colors.
fixDataStructure
Put single-set data into a form useful for multiset calculations.
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
collectGarbage
Iterative garbage collection.
simulateDatExpr5Modules
Simplified simulation of expression data
scaleFreePlot
Visual check of scale-free topology
cor
Fast calculations of Pearson correlation.
redWhiteGreen
Red-white-green color sequence
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
setCorrelationPreservation
Summary correlation preservation measure
checkAdjMat
Check adjacency matrix
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
verboseScatterplot
Scatterplot annotated by regression line and p-value
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
simulateEigengeneNetwork
Simulate eigengene network from a causal model
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
adjacency
Calculate network adjacency
labelPoints
Label scatterplot points
plotColorUnderTree
Plot color rows under a dendrogram
standardColors
Colors this library uses for labeling modules.
simulateSmallLayer
Simulate small modules
metaZfunction
Meta-analysis Z statistic
softConnectivity
Calculates connectivity of a weighted network.
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
moduleEigengenes
Calculate module eigengenes.
plot.mat
Red and Green Color Image of Data Matrix
plotModuleSignificance
Barplot of module significance
signedKME
Signed eigengene-based connectivity
stdErr
Standard error of the mean of a given vector.
vectorTOM
Topological overlap for a subset of the whole set of genes
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
clusterCoef
Clustering coefficient calculation
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
AUV2predicted
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
networkScreening
Identification of genes related to a trait
rgcolors.func
Red and Green Color Specification