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WGCNA (version 0.94)
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
0.94
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
September 8th, 2010
Functions in WGCNA (0.94)
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checkSets
Check structure and retrieve sizes of a group of datasets.
checkAdjMat
Check adjacency matrix
Inline display of progress
Inline display of progress
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
blockwiseConsensusModules
Find consensus modules across several datasets.
automaticNetworkScreening
One-step automatic network gene screening
TOMsimilarityFromExpr
Topological overlap matrix
adjacency
Calculate network adjacency
goodSamples
Filter samples with too many missing entries
labels2colors
Convert numerical labels to colors.
clusterCoef
Clustering coefficient calculation
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
numbers2colors
Color representation for a numeric variable
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
plotEigengeneNetworks
Eigengene network plot
greenWhiteRed
Green-white-red color sequence
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
keepCommonProbes
Keep probes that are shared among given data sets
corPredictionSuccess
Qunatification of success of gene screening
correlationPreservation
Preservation of eigengene correlations
collapseRows
Collapse Rows in Numeric Matrix
plot.cor
Red and Green Color Image of Correlation Matrix
fixDataStructure
Put single-set data into a form useful for multiset calculations.
WGCNA-package
Weighted Gene Co-Expression Network Analysis
networkScreeningGS
Network gene screening with an external gene significance measure
redWhiteGreen
Red-white-green color sequence
labeledHeatmap
Produce a labeled heatmap plot
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
plotModuleSignificance
Barplot of module significance
nPresent
Number of present data entries.
GTOMdist
Generalized Topological Overlap Measure
exportNetworkToCytoscape
Export network to Cytoscape
addErrorBars
Add error bars to a barplot.
corPvalueStudent
Student asymptotic p-value for correlation
networkScreening
Identification of genes related to a trait
goodGenes
Filter genes with too many missing entries
labeledBarplot
Barplot with text or color labels.
labelPoints
Label scatterplot points
stat.diag.da
Diagonal Discriminant Analysis
unsignedAdjacency
Calculation of unsigned adjacency
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
exportNetworkToVisANT
Export network data in format readable by VisANT
rgcolors.func
Red and Green Color Specification
alignExpr
Align expression data with given vector
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
simulateSmallLayer
Simulate small modules
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
metaZfunction
Meta-analysis Z statistic
AUV2predicted
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
addTraitToMEs
Add trait information to multi-set module eigengene structure
intramodularConnectivity
Calculation of intramodular connectivity
plot.mat
Red and Green Color Image of Data Matrix
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
simulateModule
Simulate a gene co-expression module
projectiveKMeans
Projective K-means (pre-)clustering of expression data
hubGeneSignificance
Hubgene significance
overlapTable
Calculate overlap of modules
plotDendroAndColors
Dendrogram plot with color annotation of objects
multiSetMEs
Calculate module eigengenes.
cutreeStaticColor
Constant height tree cut using color labels
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
cor
Fast calculations of Pearson correlation.
networkConcepts
Calculations of network concepts
simulateDatExpr
Simulation of expression data
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
cutreeStatic
Constant-height tree cut
propVarExplained
Proportion of variance explained by eigengenes.
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
randIndex
Rand index of two partitions
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
modulePreservation
Calculation of module preservation statistics
normalizeLabels
Transform numerical labels into normal order.
spaste
Space-less paste
standardColors
Colors this library uses for labeling modules.
simulateEigengeneNetwork
Simulate eigengene network from a causal model
setCorrelationPreservation
Summary correlation preservation measure
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
na
Basic Statistical Functions for Handling Missing Values
dynamicMergeCut
Threshold for module merging
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
collectGarbage
Iterative garbage collection.
greenBlackRed
Green-black-red color sequence
plotColorUnderTree
Plot color rows under a dendrogram
moduleNumber
Fixed-height cut of a dendrogram.
subsetTOM
Topological overlap for a subset of a whole set of genes
signedKME
Signed eigengene-based connectivity
plotNetworkHeatmap
Network heatmap plot
preservationNetworkConnectivity
Network preservation calculations
stdErr
Standard error of the mean of a given vector.
sizeGrWindow
Opens a graphics window with specified dimensions
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
plotMEpairs
Pairwise scatterplots of eigengenes
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
standardScreeningNumericTrait
Standard screening for numeric traits
simulateMultiExpr
Simulate multi-set expression data
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
simulateDatExpr5Modules
Simplified simulation of expression data
signumAdjacencyFunction
Hard-thresholding adjacency function
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
softConnectivity
Calculates connectivity of a weighted network.
corAndPvalue
Calculation of correlations and associated p-values
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
scaleFreePlot
Visual check of scale-free topology
vectorTOM
Topological overlap for a subset of the whole set of genes
standardScreeningBinaryTrait
Standard screening for binatry traits
stat.bwss
Between and Within Group Sum of Squares Calculation
addGrid
Add grid lines to an existing plot.
goodGenesMS
Filter genes with too many missing entries across multiple sets
bicor
Biweight Midcorrelation
colQuantileC
Fast colunm-wise quantile of a matrix.
moduleEigengenes
Calculate module eigengenes.
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
corPvalueFisher
Fisher's asymptotic p-value for correlation
TOMplot
Graphical representation of the Topological Overlap Matrix
blockwiseModules
Automatic network construction and module detection
matchLabels
Relabel module labels to best match the given reference labels
displayColors
Show colors used to label modules
mergeCloseModules
Merge close modules in gene expression data
orderMEs
Put close eigenvectors next to each other
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
relativeCorPredictionSuccess
Compare prediction success
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
verboseScatterplot
Scatterplot annotated by regression line and p-value