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WGCNA (version 0.93)
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
11,522
Version
0.93
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
August 26th, 2010
Functions in WGCNA (0.93)
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greenWhiteRed
Green-white-red color sequence
collapseRows
Collapse Rows in Numeric Matrix
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
networkScreeningGS
Network gene screening with an external gene significance measure
TOMplot
Graphical representation of the Topological Overlap Matrix
AUV2predicted
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
modulePreservation
Calculation of module preservation statistics
exportNetworkToVisANT
Export network data in format readable by VisANT
corAndPvalue
Calculation of correlations and associated p-values
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
WGCNA-package
Weighted Gene Co-Expression Network Analysis
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
plotColorUnderTree
Plot color rows under a dendrogram
corPvalueStudent
Student asymptotic p-value for correlation
automaticNetworkScreening
One-step automatic network gene screening
clusterCoef
Clustering coefficient calculation
corPredictionSuccess
Qunatification of success of gene screening
addErrorBars
Add error bars to a barplot.
labeledBarplot
Barplot with text or color labels.
goodGenes
Filter genes with too many missing entries
cutreeStaticColor
Constant height tree cut using color labels
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
cor
Fast calculations of Pearson correlation.
propVarExplained
Proportion of variance explained by eigengenes.
metaZfunction
Meta-analysis Z statistic
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
alignExpr
Align expression data with given vector
mergeCloseModules
Merge close modules in gene expression data
adjacency
Calculate network adjacency
GTOMdist
Generalized Topological Overlap Measure
preservationNetworkConnectivity
Network preservation calculations
simulateEigengeneNetwork
Simulate eigengene network from a causal model
blockwiseConsensusModules
Find consensus modules across several datasets.
displayColors
Show colors used to label modules
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
randIndex
Rand index of two partitions
correlationPreservation
Preservation of eigengene correlations
blockwiseModules
Automatic network construction and module detection
networkConcepts
Calculations of network concepts
signumAdjacencyFunction
Hard-thresholding adjacency function
exportNetworkToCytoscape
Export network to Cytoscape
fixDataStructure
Put single-set data into a form useful for multiset calculations.
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
addTraitToMEs
Add trait information to multi-set module eigengene structure
addGrid
Add grid lines to an existing plot.
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
greenBlackRed
Green-black-red color sequence
corPvalueFisher
Fisher's asymptotic p-value for correlation
moduleNumber
Fixed-height cut of a dendrogram.
simulateModule
Simulate a gene co-expression module
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
setCorrelationPreservation
Summary correlation preservation measure
simulateDatExpr5Modules
Simplified simulation of expression data
overlapTable
Calculate overlap of modules
labeledHeatmap
Produce a labeled heatmap plot
relativeCorPredictionSuccess
Compare prediction success
bicor
Biweight Midcorrelation
keepCommonProbes
Keep probes that are shared among given data sets
labels2colors
Convert numerical labels to colors.
plotNetworkHeatmap
Network heatmap plot
hubGeneSignificance
Hubgene significance
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
stat.bwss
Between and Within Group Sum of Squares Calculation
goodSamples
Filter samples with too many missing entries
simulateSmallLayer
Simulate small modules
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
collectGarbage
Iterative garbage collection.
colQuantileC
Fast colunm-wise quantile of a matrix.
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
labelPoints
Label scatterplot points
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
plotDendroAndColors
Dendrogram plot with color annotation of objects
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
signedKME
Signed eigengene-based connectivity
networkScreening
Identification of genes related to a trait
Inline display of progress
Inline display of progress
plotModuleSignificance
Barplot of module significance
multiSetMEs
Calculate module eigengenes.
rgcolors.func
Red and Green Color Specification
moduleEigengenes
Calculate module eigengenes.
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
standardScreeningBinaryTrait
Standard screening for binatry traits
standardScreeningNumericTrait
Standard screening for numeric traits
plot.cor
Red and Green Color Image of Correlation Matrix
plotMEpairs
Pairwise scatterplots of eigengenes
matchLabels
Relabel module labels to best match the given reference labels
redWhiteGreen
Red-white-green color sequence
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
numbers2colors
Color representation for a numeric variable
projectiveKMeans
Projective K-means (pre-)clustering of expression data
plot.mat
Red and Green Color Image of Data Matrix
sizeGrWindow
Opens a graphics window with specified dimensions
verboseScatterplot
Scatterplot annotated by regression line and p-value
plotEigengeneNetworks
Eigengene network plot
checkSets
Check structure and retrieve sizes of a group of datasets.
dynamicMergeCut
Threshold for module merging
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
spaste
Space-less paste
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
subsetTOM
Topological overlap for a subset of a whole set of genes
orderMEs
Put close eigenvectors next to each other
standardColors
Colors this library uses for labeling modules.
scaleFreePlot
Visual check of scale-free topology
vectorTOM
Topological overlap for a subset of the whole set of genes
stdErr
Standard error of the mean of a given vector.
normalizeLabels
Transform numerical labels into normal order.
simulateDatExpr
Simulation of expression data
na
Basic Statistical Functions for Handling Missing Values
checkAdjMat
Check adjacency matrix
cutreeStatic
Constant-height tree cut
goodGenesMS
Filter genes with too many missing entries across multiple sets
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
nPresent
Number of present data entries.
softConnectivity
Calculates connectivity of a weighted network.
simulateMultiExpr
Simulate multi-set expression data
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
TOMsimilarityFromExpr
Topological overlap matrix
intramodularConnectivity
Calculation of intramodular connectivity
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
stat.diag.da
Diagonal Discriminant Analysis
unsignedAdjacency
Calculation of unsigned adjacency