Man pages for nosarcasm/WGCNA
Weighted Correlation Network Analysis

accuracyMeasuresAccuracy measures for a 2x2 confusion matrix or for vectors...
addErrorBarsAdd error bars to a barplot.
addGridAdd grid lines to an existing plot.
addGuideLinesAdd vertical "guide lines" to a dendrogram plot
addTraitToMEsAdd trait information to multi-set module eigengene structure
adjacencyCalculate network adjacency
adjacency.polyRegAdjacency matrix based on polynomial regression
adjacency.splineRegCalculate network adjacency based on natural cubic spline...
AFcorMIPrediction of Weighted Mutual Information Adjacency Matrix by...
alignExprAlign expression data with given vector
allocateJobsDivide tasks among workers
allowWGCNAThreadsAllow and disable multi-threading for certain WGCNA...
automaticNetworkScreeningOne-step automatic network gene screening
automaticNetworkScreeningGSOne-step automatic network gene screening with external gene...
BD.getDataVarious basic operations on 'BlockwiseData' objects.
bicorBiweight Midcorrelation
bicorAndPvalueCalculation of biweight midcorrelations and associated...
bicovWeightsWeights used in biweight midcovariance
blockSizeAttempt to calculate an appropriate block size to maximize...
blockwiseConsensusModulesFind consensus modules across several datasets.
blockwiseIndividualTOMsCalculation of block-wise topological overlaps
blockwiseModulesAutomatic network construction and module detection
BloodListsBlood Cell Types with Corresponding Gene Markers
blueWhiteRedBlue-white-red color sequence
BrainListsBrain-Related Categories with Corresponding Gene Markers
BrainRegionMarkersGene Markers for Regions of the Human Brain
branchEigengeneDissimBranch dissimilarity based on eigennodes (eigengenes).
branchSplitBranch split.
branchSplit.dissimBranch split based on dissimilarity.
branchSplitFromStabilityLabelsBranch split (dissimilarity) statistics derived from labels...
checkAdjMatCheck adjacency matrix
checkSetsCheck structure and retrieve sizes of a group of datasets.
chooseOneHubInEachModuleChooses a single hub gene in each module
chooseTopHubInEachModuleChooses the top hub gene in each module
clusterCoefClustering coefficient calculation
coClusteringCo-clustering measure of cluster preservation between two...
coClustering.permutationTestPermutation test for co-clustering
collapseRowsSelect one representative row per group
collapseRowsUsingKMESelects one representative row per group based on kME
collectGarbageIterative garbage collection.
colQuantileCFast colunm- and row-wise quantile of a matrix.
conformityBasedNetworkConceptsCalculation of conformity-based network concepts.
conformityDecompositionConformity and module based decomposition of a network...
consensusCalculationCalculation of a (single) consenus with optional data...
consensusDissTOMandTreeConsensus clustering based on topological overlap and...
consensusKMECalculate consensus kME (eigengene-based connectivities)...
consensusMEDissimilarityConsensus dissimilarity of module eigengenes.
consensusOrderMEsPut close eigenvectors next to each other in several sets.
consensusProjectiveKMeansConsensus projective K-means (pre-)clustering of expression...
consensusRepresentativesConsensus selection of group representatives
consensusTOMConsensus network (topological overlap).
corFast calculations of Pearson correlation.
corAndPvalueCalculation of correlations and associated p-values
corPredictionSuccessQunatification of success of gene screening
corPvalueFisherFisher's asymptotic p-value for correlation
corPvalueStudentStudent asymptotic p-value for correlation
correlationPreservationPreservation of eigengene correlations
coxRegressionResidualsDeviance- and martingale residuals from a Cox regression...
cutreeStaticConstant-height tree cut
cutreeStaticColorConstant height tree cut using color labels
displayColorsShow colors used to label modules
dynamicMergeCutThreshold for module merging
empiricalBayesLMEmpirical Bayes-moderated adjustment for unwanted covariates
exportNetworkToCytoscapeExport network to Cytoscape
exportNetworkToVisANTExport network data in format readable by VisANT
fixDataStructurePut single-set data into a form useful for multiset...
formatLabelsBreak long character strings into multiple lines
fundamentalNetworkConceptsCalculation of fundamental network concepts from an adjacency...
GOenrichmentAnalysisCalculation of GO enrichment (experimental)
goodGenesFilter genes with too many missing entries
goodGenesMSFilter genes with too many missing entries across multiple...
goodSamplesFilter samples with too many missing entries
goodSamplesGenesIterative filtering of samples and genes with too many...
goodSamplesGenesMSIterative filtering of samples and genes with too many...
goodSamplesMSFilter samples with too many missing entries across multiple...
greenBlackRedGreen-black-red color sequence
greenWhiteRedGreen-white-red color sequence
GTOMdistGeneralized Topological Overlap Measure
hierarchicalConsensusCalculationHierarchical consensus calculation
hierarchicalConsensusKMECalculation of measures of fuzzy module membership (KME) in...
hierarchicalConsensusMEDissimilarityHierarchical consensus calculation of module eigengene...
hierarchicalConsensusModulesHierarchical consensus network construction and module...
hierarchicalConsensusTOMCalculation of hierarchical consensus topological overlap...
hierarchicalMergeCloseModulesMerge close (similar) hierarchical consensus modules
hubGeneSignificanceHubgene significance
ImmunePathwayListsImmune Pathways with Corresponding Gene Markers
imputeByModuleImpute missing data separately in each module
individualTOMsCalculate individual correlation network matrices
initProgIndInline display of progress
intramodularConnectivityCalculation of intramodular connectivity
isMultiDataDetermine whether the supplied object is a valid multiData...
keepCommonProbesKeep probes that are shared among given data sets
kMEcomparisonScatterplotFunction to plot kME values between two comparable data sets.
labeledBarplotBarplot with text or color labels.
labeledHeatmapProduce a labeled heatmap plot
labeledHeatmap.multiPageLabeled heatmap divided into several separate plots.
labelPointsLabel scatterplot points
labels2colorsConvert numerical labels to colors.
list2multiDataConvert a list to a multiData structure and vice-versa.
lowerTri2matrixReconstruct a symmetric matrix from a distance...
matchLabelsRelabel module labels to best match the given reference...
matrixToNetworkConstruct a network from a matrix
mergeCloseModulesMerge close modules in gene expression data
metaAnalysisMeta-analysis of binary and continuous variables
metaZfunctionMeta-analysis Z statistic
minWhichMinFast joint calculation of row- or column-wise minima and...
moduleColor.getMEprefixGet the prefix used to label module eigengenes.
moduleEigengenesCalculate module eigengenes.
moduleMergeUsingKMEMerge modules and reassign genes using kME.
moduleNumberFixed-height cut of a dendrogram.
modulePreservationCalculation of module preservation statistics
mtd.applyApply a function to each set in a multiData structure.
mtd.mapplyApply a function to elements of given multiData structures.
mtd.rbindSelfTurn a multiData structure into a single matrix or data...
mtd.setAttrSet attributes on each component of a multiData structure
mtd.setColnamesGet and set column names in a multiData structure.
mtd.simplifyIf possible, simplify a multiData structure to a...
mtd.subsetSubset rows and columns in a multiData structure
multiDataCreate a multiData structure.
multiData.eigengeneSignificanceEigengene significance across multiple sets
multiGSubAnalogs of grep(l) and (g)sub for multiple patterns and...
multiSetMEsCalculate module eigengenes.
multiUnionUnion and intersection of multiple sets
mutualInfoAdjacencyCalculate weighted adjacency matrices based on mutual...
nearestCentroidPredictorNearest centroid predictor
nearestNeighborConnectivityConnectivity to a constant number of nearest neighbors
nearestNeighborConnectivityMSConnectivity to a constant number of nearest neighbors across...
networkConceptsCalculations of network concepts
networkScreeningIdentification of genes related to a trait
networkScreeningGSNetwork gene screening with an external gene significance...
newBlockInformationCreate a list holding information about dividing data into...
newBlockwiseDataCreate, merge and expand BlockwiseData objects
newConsensusOptionsCreate a list holding consensus calculation options.
newConsensusTreeCreate a new consensus tree
newCorrelationOptionsCreates a list of correlation options.
newNetworkOptionsCreate a list of network construction arguments (options).
normalizeLabelsTransform numerical labels into normal order.
nPresentNumber of present data entries.
nSetsNumber of sets in a multi-set variable
numbers2colorsColor representation for a numeric variable
orderBranchesUsingHubGenesOptimize dendrogram using branch swaps and reflections.
orderMEsPut close eigenvectors next to each other
orderMEsByHierarchicalConsensusOrder module eigengenes by their hierarchical consensus...
overlapTableCalculate overlap of modules
overlapTableUsingKMEDetermines significant overlap between modules in two...
pickHardThresholdAnalysis of scale free topology for hard-thresholding.
pickSoftThresholdAnalysis of scale free topology for soft-thresholding
plotClusterTreeSamplesAnnotated clustering dendrogram of microarray samples
plotColorUnderTreePlot color rows in a given order, for example under a...
plotCorRed and Green Color Image of Correlation Matrix
plotDendroAndColorsDendrogram plot with color annotation of objects
plotEigengeneNetworksEigengene network plot
plotMatRed and Green Color Image of Data Matrix
plotMEpairsPairwise scatterplots of eigengenes
plotModuleSignificanceBarplot of module significance
plotMultiHistPlot multiple histograms in a single plot
plotNetworkHeatmapNetwork heatmap plot
populationMeansInAdmixtureEstimate the population-specific mean values in an admixed...
pquantileParallel quantile, median, mean
prepCommaPrepend a comma to a non-empty string
prependZerosPad numbers with leading zeros to specified total width
preservationNetworkConnectivityNetwork preservation calculations
projectiveKMeansProjective K-means (pre-)clustering of expression data
proportionsInAdmixtureEstimate the proportion of pure populations in an admixed...
propVarExplainedProportion of variance explained by eigengenes.
pruneAndMergeConsensusModulesIterative pruning and merging of (hierarchical) consensus...
pruneConsensusModulesPrune (hierarchical) consensus modules by removing genes with...
PWListsPathways with Corresponding Gene Markers - Compiled by Mike...
qvalueEstimate the q-values for a given set of p-values
qvalue.restrictedqvalue convenience wrapper
randIndexRand index of two partitions
rankPvalueEstimate the p-value for ranking consistently high (or low)...
recutBlockwiseTreesRepeat blockwise module detection from pre-calculated data
recutConsensusTreesRepeat blockwise consensus module detection from...
redWhiteGreenRed-white-green color sequence
relativeCorPredictionSuccessCompare prediction success
removeGreyMERemoves the grey eigengene from a given collection of...
removePrincipalComponentsRemove leading principal components from data
replaceMissingReplace missing values with a constant.
returnGeneSetsAsListReturn pre-defined gene lists in several biomedical...
rgcolors.funcRed and Green Color Specification
sampledBlockwiseModulesBlockwise module identification in sampled data
sampledHierarchicalConsensusModulesHierarchical consensus module identification in sampled data
scaleFreeFitIndexCalculation of fitting statistics for evaluating scale free...
scaleFreePlotVisual check of scale-free topology
SCsListsStem Cell-Related Genes with Corresponding Gene Markers
selectFewestConsensusMissingSelect columns with the lowest consensus number of missing...
setCorrelationPreservationSummary correlation preservation measure
shortenStringsShorten given character strings by truncating at a suitable...
sigmoidAdjacencyFunctionSigmoid-type adacency function.
signedKMESigned eigengene-based connectivity
signumAdjacencyFunctionHard-thresholding adjacency function
simpleConsensusCalculationSimple calculation of a single consenus
simpleHierarchicalConsensusCalculationSimple hierarchical consensus calculation
simulateDatExprSimulation of expression data
simulateDatExpr5ModulesSimplified simulation of expression data
simulateEigengeneNetworkSimulate eigengene network from a causal model
simulateModuleSimulate a gene co-expression module
simulateMultiExprSimulate multi-set expression data
simulateSmallLayerSimulate small modules
sizeGrWindowOpens a graphics window with specified dimensions
softConnectivityCalculates connectivity of a weighted network.
spasteSpace-less paste
standardColorsColors this library uses for labeling modules.
standardScreeningBinaryTraitStandard screening for binatry traits
standardScreeningCensoredTimeStandard Screening with regard to a Censored Time Variable
standardScreeningNumericTraitStandard screening for numeric traits
stdErrStandard error of the mean of a given vector.
stratifiedBarplotBar plots of data across two splitting parameters
subsetTOMTopological overlap for a subset of a whole set of genes
swapTwoBranchesSelect, swap, or reflect branches in a dendrogram.
TOMplotGraphical representation of the Topological Overlap Matrix
TOMsimilarityTopological overlap matrix similarity and dissimilarity
TOMsimilarityFromExprTopological overlap matrix
transposeBigDataTranspose a big matrix or data frame
TrueTraitEstimate the true trait underlying a list of surrogate...
unsignedAdjacencyCalculation of unsigned adjacency
userListEnrichmentMeasure enrichment between inputted and user-defined lists
vectorizeMatrixTurn a matrix into a vector of non-redundant components
vectorTOMTopological overlap for a subset of the whole set of genes
verboseBarplotBarplot with error bars, annotated by Kruskal-Wallis or ANOVA...
verboseBoxplotBoxplot annotated by a Kruskal-Wallis p-value
verboseIplotScatterplot with density
verboseScatterplotScatterplot annotated by regression line and p-value
votingLinearPredictorVoting linear predictor
WGCNA-packageWeighted Gene Co-Expression Network Analysis
nosarcasm/WGCNA documentation built on Feb. 21, 2018, 12:22 a.m.