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WGCNA (version 0.92-3)
Weighted Gene Co-Expression Network Analysis
Description
Functions necessary to perform Weighted Gene Co-Expression Network Analysis
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0.92-3
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Install
install.packages('WGCNA')
Monthly Downloads
18,389
Version
0.92-3
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
July 26th, 2010
Functions in WGCNA (0.92-3)
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addGrid
Add grid lines to an existing plot.
TOMsimilarityFromExpr
Topological overlap matrix
WGCNA-package
Weighted Gene Co-Expression Network Analysis
greenBlackRed
Green-black-red color sequence
redWhiteGreen
Red-white-green color sequence
automaticNetworkScreening
One-step automatic network gene screening
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
networkScreeningGS
Network gene screening with an external gene significance measure
greenWhiteRed
Green-white-red color sequence
corPredictionSuccess
Qunatification of success of gene screening
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
plot.cor
Red and Green Color Image of Correlation Matrix
cutreeStatic
Constant-height tree cut
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
GTOMdist
Generalized Topological Overlap Measure
alignExpr
Align expression data with given vector
labelPoints
Label scatterplot points
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
blockwiseModules
Automatic network construction and module detection
goodSamples
Filter samples with too many missing entries
preservationNetworkConnectivity
Network preservation calculations
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
plotDendroAndColors
Dendrogram plot with color annotation of objects
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
checkSets
Check structure and retrieve sizes of a group of datasets.
plotMEpairs
Pairwise scatterplots of eigengenes
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
numbers2colors
Color representation for a numeric variable
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
exportNetworkToVisANT
Export network data in format readable by VisANT
blockwiseConsensusModules
Find consensus modules across several datasets.
vectorTOM
Topological overlap for a subset of the whole set of genes
simulateMultiExpr
Simulate multi-set expression data
simulateSmallLayer
Simulate small modules
colQuantileC
Fast colunm-wise quantile of a matrix.
goodGenes
Filter genes with too many missing entries
metaZfunction
Meta-analysis Z statistic
checkAdjMat
Check adjacency matrix
relativeCorPredictionSuccess
Compare prediction success
multiSetMEs
Calculate module eigengenes.
addTraitToMEs
Add trait information to multi-set module eigengene structure
simulateModule
Simulate a gene co-expression module
modulePreservation
Calculation of module preservation statistics
exportNetworkToCytoscape
Export network to Cytoscape
verboseScatterplot
Scatterplot annotated by regression line and p-value
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
correlationPreservation
Preservation of eigengene correlations
addErrorBars
Add error bars to a barplot.
nPresent
Number of present data entries.
plotEigengeneNetworks
Eigengene network plot
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
subsetTOM
Topological overlap for a subset of a whole set of genes
corAndPvalue
Calculation of correlations and associated p-values
cutreeStaticColor
Constant height tree cut using color labels
cor
Fast calculations of Pearson correlation.
clusterCoef
Clustering coefficient calculation
mergeCloseModules
Merge close modules in gene expression data
displayColors
Show colors used to label modules
sizeGrWindow
Opens a graphics window with specified dimensions
moduleEigengenes
Calculate module eigengenes.
overlapTable
Calculate overlap of modules
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
labels2colors
Convert numerical labels to colors.
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
hubGeneSignificance
Hubgene significance
simulateDatExpr5Modules
Simplified simulation of expression data
TOMplot
Graphical representation of the Topological Overlap Matrix
matchLabels
Relabel module labels to best match the given reference labels
keepCommonProbes
Keep probes that are shared among given data sets
networkConcepts
Calculations of network concepts
standardColors
Colors this library uses for labeling modules.
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
stat.bwss
Between and Within Group Sum of Squares Calculation
moduleNumber
Fixed-height cut of a dendrogram.
standardScreeningNumericTrait
Standard screening for numeric traits
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
dynamicMergeCut
Threshold for module merging
corPvalueStudent
Student asymptotic p-value for correlation
plotColorUnderTree
Plot color rows under a dendrogram
labeledHeatmap
Produce a labeled heatmap plot
fixDataStructure
Put single-set data into a form useful for multiset calculations.
orderMEs
Put close eigenvectors next to each other
projectiveKMeans
Projective K-means (pre-)clustering of expression data
scaleFreePlot
Visual check of scale-free topology
plotNetworkHeatmap
Network heatmap plot
softConnectivity
Calculates connectivity of a weighted network.
normalizeLabels
Transform numerical labels into normal order.
plot.mat
Red and Green Color Image of Data Matrix
labeledBarplot
Barplot with text or color labels.
collapseRows
Collapse Rows in Numeric Matrix
intramodularConnectivity
Calculation of intramodular connectivity
setCorrelationPreservation
Summary correlation preservation measure
simulateEigengeneNetwork
Simulate eigengene network from a causal model
stat.diag.da
Diagonal Discriminant Analysis
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
randIndex
Rand index of two partitions
collectGarbage
Iterative garbage collection.
rgcolors.func
Red and Green Color Specification
plotModuleSignificance
Barplot of module significance
standardScreeningBinaryTrait
Standard screening for binatry traits
propVarExplained
Proportion of variance explained by eigengenes.
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
goodGenesMS
Filter genes with too many missing entries across multiple sets
signedKME
Signed eigengene-based connectivity
stdErr
Standard error of the mean of a given vector.
unsignedAdjacency
Calculation of unsigned adjacency
simulateDatExpr
Simulation of expression data
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
Inline display of progress
Inline display of progress
spaste
Space-less paste
signumAdjacencyFunction
Hard-thresholding adjacency function
corPvalueFisher
Fisher's asymptotic p-value for correlation
na
Basic Statistical Functions for Handling Missing Values
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
bicor
Biweight Midcorrelation
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
adjacency
Calculate network adjacency
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
networkScreening
Identification of genes related to a trait