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WGCNA (version 0.98)
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
0.98
License
GPL (>= 2)
Maintainer
Peter Langfelder
Last Published
November 13th, 2010
Functions in WGCNA (0.98)
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consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
TOMsimilarityFromExpr
Topological overlap matrix
adjacency
Calculate network adjacency
GOenrichmentAnalysis
Calculation of GO enrichment (experimental)
blockwiseConsensusModules
Find consensus modules across several datasets.
alignExpr
Align expression data with given vector
collapseRows
Select one representative row per group
TOMsimilarity
Topological overlap matrix similarity and dissimilarity
checkSets
Check structure and retrieve sizes of a group of datasets.
addTraitToMEs
Add trait information to multi-set module eigengene structure
labels2colors
Convert numerical labels to colors.
rgcolors.func
Red and Green Color Specification
cor
Fast calculations of Pearson correlation.
matchLabels
Relabel module labels to best match the given reference labels
collectGarbage
Iterative garbage collection.
consensusOrderMEs
Put close eigenvectors next to each other in several sets.
dynamicMergeCut
Threshold for module merging
multiSetMEs
Calculate module eigengenes.
corPvalueStudent
Student asymptotic p-value for correlation
automaticNetworkScreening
One-step automatic network gene screening
metaZfunction
Meta-analysis Z statistic
vectorTOM
Topological overlap for a subset of the whole set of genes
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
bicor
Biweight Midcorrelation
modulePreservation
Calculation of module preservation statistics
simulateDatExpr5Modules
Simplified simulation of expression data
correlationPreservation
Preservation of eigengene correlations
goodSamplesGenes
Iterative filtering of samples and genes with too many missing entries
greenBlackRed
Green-black-red color sequence
randIndex
Rand index of two partitions
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
exportNetworkToCytoscape
Export network to Cytoscape
goodGenesMS
Filter genes with too many missing entries across multiple sets
colQuantileC
Fast colunm-wise quantile of a matrix.
clusterCoef
Clustering coefficient calculation
goodSamplesGenesMS
Iterative filtering of samples and genes with too many missing entries across multiple data sets
verboseScatterplot
Scatterplot annotated by regression line and p-value
networkScreening
Identification of genes related to a trait
mergeCloseModules
Merge close modules in gene expression data
labelPoints
Label scatterplot points
propVarExplained
Proportion of variance explained by eigengenes.
corAndPvalue
Calculation of correlations and associated p-values
networkConcepts
Calculations of network concepts
signumAdjacencyFunction
Hard-thresholding adjacency function
exportNetworkToVisANT
Export network data in format readable by VisANT
standardScreeningBinaryTrait
Standard screening for binatry traits
pickSoftThreshold
Analysis of scale free topology for soft-thresholding
AUV2predicted
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
relativeCorPredictionSuccess
Compare prediction success
goodSamplesMS
Filter samples with too many missing entries across multiple data sets
fixDataStructure
Put single-set data into a form useful for multiset calculations.
simulateModule
Simulate a gene co-expression module
plot.mat
Red and Green Color Image of Data Matrix
verboseBarplot
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
moduleNumber
Fixed-height cut of a dendrogram.
hubGeneSignificance
Hubgene significance
Inline display of progress
Inline display of progress
moduleEigengenes
Calculate module eigengenes.
plotColorUnderTree
Plot color rows under a dendrogram
simulateEigengeneNetwork
Simulate eigengene network from a causal model
displayColors
Show colors used to label modules
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
goodGenes
Filter genes with too many missing entries
cutreeStatic
Constant-height tree cut
addGrid
Add grid lines to an existing plot.
keepCommonProbes
Keep probes that are shared among given data sets
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
scaleFreeFitIndex
Calculation of fitting statistics for evaluating scale free topology fit.
orderMEs
Put close eigenvectors next to each other
GTOMdist
Generalized Topological Overlap Measure
labeledBarplot
Barplot with text or color labels.
WGCNA-package
Weighted Gene Co-Expression Network Analysis
preservationNetworkConnectivity
Network preservation calculations
pickHardThreshold
Analysis of scale free topology for hard-thresholding.
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
blockwiseModules
Automatic network construction and module detection
numbers2colors
Color representation for a numeric variable
normalizeLabels
Transform numerical labels into normal order.
plotNetworkHeatmap
Network heatmap plot
simulateDatExpr
Simulation of expression data
overlapTable
Calculate overlap of modules
simulateSmallLayer
Simulate small modules
labeledHeatmap
Produce a labeled heatmap plot
addErrorBars
Add error bars to a barplot.
addGuideLines
Add vertical ``guide lines'' to a dendrogram plot
goodSamples
Filter samples with too many missing entries
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
recutBlockwiseTrees
Repeat blockwise module detection from pre-calculated data
stat.diag.da
Diagonal Discriminant Analysis
greenWhiteRed
Green-white-red color sequence
cutreeStaticColor
Constant height tree cut using color labels
stat.bwss
Between and Within Group Sum of Squares Calculation
bicorAndPvalue
Calculation of biweight midcorrelations and associated p-values
networkScreeningGS
Network gene screening with an external gene significance measure
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
signedKME
Signed eigengene-based connectivity
intramodularConnectivity
Calculation of intramodular connectivity
plotDendroAndColors
Dendrogram plot with color annotation of objects
pquantile
Parallel quantile, median, mean
removeGreyME
Removes the grey eigengene from a given collection of eigengenes.
na
Basic Statistical Functions for Handling Missing Values
projectiveKMeans
Projective K-means (pre-)clustering of expression data
stdErr
Standard error of the mean of a given vector.
nPresent
Number of present data entries.
unsignedAdjacency
Calculation of unsigned adjacency
scaleFreePlot
Visual check of scale-free topology
verboseBoxplot
Boxplot annotated by a Kruskal-Wallis p-value
spaste
Space-less paste
redWhiteGreen
Red-white-green color sequence
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
vectorizeMatrix
Turn a matrix into a vector of non-redundant components
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
softConnectivity
Calculates connectivity of a weighted network.
standardScreeningNumericTrait
Standard screening for numeric traits
simulateMultiExpr
Simulate multi-set expression data
sizeGrWindow
Opens a graphics window with specified dimensions
plotMEpairs
Pairwise scatterplots of eigengenes
plotEigengeneNetworks
Eigengene network plot
standardColors
Colors this library uses for labeling modules.
subsetTOM
Topological overlap for a subset of a whole set of genes
plotModuleSignificance
Barplot of module significance
setCorrelationPreservation
Summary correlation preservation measure
plotClusterTreeSamples
Annotated clustering dendrogram of microarray samples
TOMplot
Graphical representation of the Topological Overlap Matrix
recutConsensusTrees
Repeat blockwise consensus module detection from pre-calculated data
checkAdjMat
Check adjacency matrix
corPvalueFisher
Fisher's asymptotic p-value for correlation
mutualInfoAdjacency
Calculate weighted adjacency matrices based on mutual information
plot.cor
Red and Green Color Image of Correlation Matrix
rankPvalue
Estimate the p-value for ranking consistently high (or low) on multiple lists
corPredictionSuccess
Qunatification of success of gene screening