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WGCNA (version 0.99)
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
0.99
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
December 22nd, 2010
Functions in WGCNA (0.99)
Search all functions
checkSets
Check structure and retrieve sizes of a group of datasets.
signumAdjacencyFunction
Hard-thresholding adjacency function
addTraitToMEs
Add trait information to multi-set module eigengene structure
numbers2colors
Color representation for a numeric variable
addErrorBars
Add error bars to a barplot.
Inline display of progress
Inline display of progress
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
checkAdjMat
Check adjacency matrix
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
automaticNetworkScreening
One-step automatic network gene screening
overlapTable
Calculate overlap of modules
goodGenes
Filter genes with too many missing entries
correlationPreservation
Preservation of eigengene correlations
displayColors
Show colors used to label modules
adjacency
Calculate network adjacency
plotMEpairs
Pairwise scatterplots of eigengenes
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
plotNetworkHeatmap
Network heatmap plot
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
colQuantileC
Fast colunm-wise quantile of a matrix.
simulateModule
Simulate a gene co-expression module
corAndPvalue
Calculation of correlations and associated p-values
cor
Fast calculations of Pearson correlation.
simulateDatExpr
Simulation of expression data
exportNetworkToCytoscape
Export network to Cytoscape
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
GTOMdist
Generalized Topological Overlap Measure
TOMplot
Graphical representation of the Topological Overlap Matrix
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
bicor
Biweight Midcorrelation
networkScreeningGS
Network gene screening with an external gene significance measure
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
AUV2predicted
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
corPredictionSuccess
Qunatification of success of gene screening
WGCNA-package
Weighted Gene Co-Expression Network Analysis
modulePreservation
Calculation of module preservation statistics
labeledBarplot
Barplot with text or color labels.
blockwiseConsensusModules
Find consensus modules across several datasets.
corPvalueStudent
Student asymptotic p-value for correlation
collectGarbage
Iterative garbage collection.
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
collapseRows
Select one representative row per group
projectiveKMeans
Projective K-means (pre-)clustering of expression data
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
addGrid
Add grid lines to an existing plot.
plotColorUnderTree
Plot color rows under a dendrogram
dynamicMergeCut
Threshold for module merging
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
cutreeStaticColor
Constant height tree cut using color labels
TOMsimilarityFromExpr
Topological overlap matrix
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
plot.cor
Red and Green Color Image of Correlation Matrix
scaleFreePlot
Visual check of scale-free topology
networkConcepts
Calculations of network concepts
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
setCorrelationPreservation
Summary correlation preservation measure
keepCommonProbes
Keep probes that are shared among given data sets
alignExpr
Align expression data with given vector
greenWhiteRed
Green-white-red color sequence
networkScreening
Identification of genes related to a trait
standardColors
Colors this library uses for labeling modules.
hubGeneSignificance
Hubgene significance
plotEigengeneNetworks
Eigengene network plot
labels2colors
Convert numerical labels to colors.
na
Basic Statistical Functions for Handling Missing Values
rgcolors.func
Red and Green Color Specification
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
mergeCloseModules
Merge close modules in gene expression data
goodGenesMS
Filter genes with too many missing entries across multiple sets
goodSamples
Filter samples with too many missing entries
labelPoints
Label scatterplot points
orderMEs
Put close eigenvectors next to each other
propVarExplained
Proportion of variance explained by eigengenes.
labeledHeatmap
Produce a labeled heatmap plot
moduleEigengenes
Calculate module eigengenes.
metaZfunction
Meta-analysis Z statistic
corPvalueFisher
Fisher's asymptotic p-value for correlation
multiSetMEs
Calculate module eigengenes.
moduleNumber
Fixed-height cut of a dendrogram.
blockwiseModules
Automatic network construction and module detection
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
simulateDatExpr5Modules
Simplified simulation of expression data
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
normalizeLabels
Transform numerical labels into normal order.
pquantile
Parallel quantile, median, mean
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
sizeGrWindow
Opens a graphics window with specified dimensions
fixDataStructure
Put single-set data into a form useful for multiset calculations.
matchLabels
Relabel module labels to best match the given reference labels
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
cutreeStatic
Constant-height tree cut
signedKME
Signed eigengene-based connectivity
nPresent
Number of present data entries.
simulateSmallLayer
Simulate small modules
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
simulateEigengeneNetwork
Simulate eigengene network from a causal model
stat.diag.da
Diagonal Discriminant Analysis
stat.bwss
Between and Within Group Sum of Squares Calculation
redWhiteGreen
Red-white-green color sequence
simulateMultiExpr
Simulate multi-set expression data
relativeCorPredictionSuccess
Compare prediction success
plotModuleSignificance
Barplot of module significance
plot.mat
Red and Green Color Image of Data Matrix
vectorTOM
Topological overlap for a subset of the whole set of genes
subsetTOM
Topological overlap for a subset of a whole set of genes
softConnectivity
Calculates connectivity of a weighted network.
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
spaste
Space-less paste
verboseScatterplot
Scatterplot annotated by regression line and p-value
unsignedAdjacency
Calculation of unsigned adjacency
standardScreeningNumericTrait
Standard screening for numeric traits
stdErr
Standard error of the mean of a given vector.
standardScreeningBinaryTrait
Standard screening for binatry traits
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
clusterCoef
Clustering coefficient calculation
exportNetworkToVisANT
Export network data in format readable by VisANT
greenBlackRed
Green-black-red color sequence
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
plotDendroAndColors
Dendrogram plot with color annotation of objects
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
preservationNetworkConnectivity
Network preservation calculations
intramodularConnectivity
Calculation of intramodular connectivity
randIndex
Rand index of two partitions
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable