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WGCNA (version 0.96)
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
16,020
Version
0.96
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
September 23rd, 2010
Functions in WGCNA (0.96)
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addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
corPvalueFisher
Fisher's asymptotic p-value for correlation
cor
Fast calculations of Pearson correlation.
corAndPvalue
Calculation of correlations and associated p-values
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
collectGarbage
Iterative garbage collection.
exportNetworkToCytoscape
Export network to Cytoscape
matchLabels
Relabel module labels to best match the given reference labels
clusterCoef
Clustering coefficient calculation
greenWhiteRed
Green-white-red color sequence
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
exportNetworkToVisANT
Export network data in format readable by VisANT
scaleFreePlot
Visual check of scale-free topology
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
corPvalueStudent
Student asymptotic p-value for correlation
alignExpr
Align expression data with given vector
labeledHeatmap
Produce a labeled heatmap plot
metaZfunction
Meta-analysis Z statistic
addTraitToMEs
Add trait information to multi-set module eigengene structure
addGrid
Add grid lines to an existing plot.
pquantile
Parallel quantile, median, mean
plotModuleSignificance
Barplot of module significance
goodSamples
Filter samples with too many missing entries
Inline display of progress
Inline display of progress
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
cutreeStaticColor
Constant height tree cut using color labels
mergeCloseModules
Merge close modules in gene expression data
rgcolors.func
Red and Green Color Specification
collapseRows
Select one representative row per group
TOMsimilarityFromExpr
Topological overlap matrix
goodGenesMS
Filter genes with too many missing entries across multiple sets
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
checkAdjMat
Check adjacency matrix
intramodularConnectivity
Calculation of intramodular connectivity
bicor
Biweight Midcorrelation
correlationPreservation
Preservation of eigengene correlations
hubGeneSignificance
Hubgene significance
labeledBarplot
Barplot with text or color labels.
addErrorBars
Add error bars to a barplot.
TOMplot
Graphical representation of the Topological Overlap Matrix
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
goodGenes
Filter genes with too many missing entries
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
keepCommonProbes
Keep probes that are shared among given data sets
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
colQuantileC
Fast colunm-wise quantile of a matrix.
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
signedKME
Signed eigengene-based connectivity
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
labels2colors
Convert numerical labels to colors.
automaticNetworkScreening
One-step automatic network gene screening
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
checkSets
Check structure and retrieve sizes of a group of datasets.
multiSetMEs
Calculate module eigengenes.
nPresent
Number of present data entries.
blockwiseModules
Automatic network construction and module detection
plot.mat
Red and Green Color Image of Data Matrix
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
blockwiseConsensusModules
Find consensus modules across several datasets.
AUV2predicted
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
plotMEpairs
Pairwise scatterplots of eigengenes
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
moduleNumber
Fixed-height cut of a dendrogram.
relativeCorPredictionSuccess
Compare prediction success
plot.cor
Red and Green Color Image of Correlation Matrix
overlapTable
Calculate overlap of modules
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
networkConcepts
Calculations of network concepts
adjacency
Calculate network adjacency
fixDataStructure
Put single-set data into a form useful for multiset calculations.
cutreeStatic
Constant-height tree cut
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
randIndex
Rand index of two partitions
labelPoints
Label scatterplot points
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
orderMEs
Put close eigenvectors next to each other
displayColors
Show colors used to label modules
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
preservationNetworkConnectivity
Network preservation calculations
normalizeLabels
Transform numerical labels into normal order.
signumAdjacencyFunction
Hard-thresholding adjacency function
propVarExplained
Proportion of variance explained by eigengenes.
modulePreservation
Calculation of module preservation statistics
plotDendroAndColors
Dendrogram plot with color annotation of objects
na
Basic Statistical Functions for Handling Missing Values
plotColorUnderTree
Plot color rows under a dendrogram
projectiveKMeans
Projective K-means (pre-)clustering of expression data
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
networkScreeningGS
Network gene screening with an external gene significance measure
plotEigengeneNetworks
Eigengene network plot
stdErr
Standard error of the mean of a given vector.
simulateMultiExpr
Simulate multi-set expression data
numbers2colors
Color representation for a numeric variable
simulateDatExpr
Simulation of expression data
vectorTOM
Topological overlap for a subset of the whole set of genes
redWhiteGreen
Red-white-green color sequence
corPredictionSuccess
Qunatification of success of gene screening
simulateDatExpr5Modules
Simplified simulation of expression data
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
simulateSmallLayer
Simulate small modules
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
standardScreeningBinaryTrait
Standard screening for binatry traits
softConnectivity
Calculates connectivity of a weighted network.
standardColors
Colors this library uses for labeling modules.
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
sizeGrWindow
Opens a graphics window with specified dimensions
setCorrelationPreservation
Summary correlation preservation measure
dynamicMergeCut
Threshold for module merging
spaste
Space-less paste
stat.bwss
Between and Within Group Sum of Squares Calculation
standardScreeningNumericTrait
Standard screening for numeric traits
stat.diag.da
Diagonal Discriminant Analysis
networkScreening
Identification of genes related to a trait
simulateModule
Simulate a gene co-expression module
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
plotNetworkHeatmap
Network heatmap plot
unsignedAdjacency
Calculation of unsigned adjacency
verboseScatterplot
Scatterplot annotated by regression line and p-value
subsetTOM
Topological overlap for a subset of a whole set of genes
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
WGCNA-package
Weighted Gene Co-Expression Network Analysis
GTOMdist
Generalized Topological Overlap Measure
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
greenBlackRed
Green-black-red color sequence
moduleEigengenes
Calculate module eigengenes.
simulateEigengeneNetwork
Simulate eigengene network from a causal model