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WGCNA (version 0.95)
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
13,041
Version
0.95
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
September 17th, 2010
Functions in WGCNA (0.95)
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automaticNetworkScreening
One-step automatic network gene screening
exportNetworkToCytoscape
Export network to Cytoscape
checkSets
Check structure and retrieve sizes of a group of datasets.
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
TOMplot
Graphical representation of the Topological Overlap Matrix
intramodularConnectivity
Calculation of intramodular connectivity
corPredictionSuccess
Qunatification of success of gene screening
moduleNumber
Fixed-height cut of a dendrogram.
hubGeneSignificance
Hubgene significance
mergeCloseModules
Merge close modules in gene expression data
adjacency
Calculate network adjacency
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
addGrid
Add grid lines to an existing plot.
networkConcepts
Calculations of network concepts
WGCNA-package
Weighted Gene Co-Expression Network Analysis
addTraitToMEs
Add trait information to multi-set module eigengene structure
cutreeStaticColor
Constant height tree cut using color labels
overlapTable
Calculate overlap of modules
fixDataStructure
Put single-set data into a form useful for multiset calculations.
multiSetMEs
Calculate module eigengenes.
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
orderMEs
Put close eigenvectors next to each other
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
greenBlackRed
Green-black-red color sequence
cor
Fast calculations of Pearson correlation.
corPvalueFisher
Fisher's asymptotic p-value for correlation
plot.mat
Red and Green Color Image of Data Matrix
checkAdjMat
Check adjacency matrix
blockwiseModules
Automatic network construction and module detection
networkScreeningGS
Network gene screening with an external gene significance measure
rgcolors.func
Red and Green Color Specification
relativeCorPredictionSuccess
Compare prediction success
exportNetworkToVisANT
Export network data in format readable by VisANT
alignExpr
Align expression data with given vector
nPresent
Number of present data entries.
moduleEigengenes
Calculate module eigengenes.
goodGenes
Filter genes with too many missing entries
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
labels2colors
Convert numerical labels to colors.
redWhiteGreen
Red-white-green color sequence
softConnectivity
Calculates connectivity of a weighted network.
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
collapseRows
Select one representative row per group
addErrorBars
Add error bars to a barplot.
AUV2predicted
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
labelPoints
Label scatterplot points
simulateMultiExpr
Simulate multi-set expression data
sizeGrWindow
Opens a graphics window with specified dimensions
stat.bwss
Between and Within Group Sum of Squares Calculation
signumAdjacencyFunction
Hard-thresholding adjacency function
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
Inline display of progress
Inline display of progress
simulateEigengeneNetwork
Simulate eigengene network from a causal model
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
spaste
Space-less paste
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
correlationPreservation
Preservation of eigengene correlations
goodGenesMS
Filter genes with too many missing entries across multiple sets
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
metaZfunction
Meta-analysis Z statistic
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
cutreeStatic
Constant-height tree cut
randIndex
Rand index of two partitions
bicor
Biweight Midcorrelation
simulateSmallLayer
Simulate small modules
unsignedAdjacency
Calculation of unsigned adjacency
clusterCoef
Clustering coefficient calculation
simulateDatExpr5Modules
Simplified simulation of expression data
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
GTOMdist
Generalized Topological Overlap Measure
corAndPvalue
Calculation of correlations and associated p-values
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
plotNetworkHeatmap
Network heatmap plot
standardScreeningBinaryTrait
Standard screening for binatry traits
displayColors
Show colors used to label modules
TOMsimilarityFromExpr
Topological overlap matrix
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
dynamicMergeCut
Threshold for module merging
matchLabels
Relabel module labels to best match the given reference labels
simulateDatExpr
Simulation of expression data
blockwiseConsensusModules
Find consensus modules across several datasets.
simulateModule
Simulate a gene co-expression module
stdErr
Standard error of the mean of a given vector.
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
goodSamples
Filter samples with too many missing entries
labeledBarplot
Barplot with text or color labels.
networkScreening
Identification of genes related to a trait
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
colQuantileC
Fast colunm-wise quantile of a matrix.
corPvalueStudent
Student asymptotic p-value for correlation
plotMEpairs
Pairwise scatterplots of eigengenes
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
labeledHeatmap
Produce a labeled heatmap plot
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
plot.cor
Red and Green Color Image of Correlation Matrix
plotModuleSignificance
Barplot of module significance
plotDendroAndColors
Dendrogram plot with color annotation of objects
plotColorUnderTree
Plot color rows under a dendrogram
propVarExplained
Proportion of variance explained by eigengenes.
signedKME
Signed eigengene-based connectivity
standardColors
Colors this library uses for labeling modules.
normalizeLabels
Transform numerical labels into normal order.
subsetTOM
Topological overlap for a subset of a whole set of genes
projectiveKMeans
Projective K-means (pre-)clustering of expression data
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
verboseScatterplot
Scatterplot annotated by regression line and p-value
setCorrelationPreservation
Summary correlation preservation measure
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
preservationNetworkConnectivity
Network preservation calculations
na
Basic Statistical Functions for Handling Missing Values
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
numbers2colors
Color representation for a numeric variable
plotEigengeneNetworks
Eigengene network plot
keepCommonProbes
Keep probes that are shared among given data sets
stat.diag.da
Diagonal Discriminant Analysis
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
modulePreservation
Calculation of module preservation statistics
greenWhiteRed
Green-white-red color sequence
standardScreeningNumericTrait
Standard screening for numeric traits
collectGarbage
Iterative garbage collection.