AFcorMI Prediction of Weighted Mutual Information
Adjacency Matrix by Correlation
BD.getData Various basic operations on 'BlockwiseData'
objects.
BloodLists Blood Cell Types with Corresponding Gene
Markers
BrainLists Brain-Related Categories with Corresponding
Gene Markers
BrainRegionMarkers Gene Markers for Regions of the Human Brain
GOenrichmentAnalysis Calculation of GO enrichment (experimental)
GTOMdist Generalized Topological Overlap Measure
ImmunePathwayLists Immune Pathways with Corresponding Gene Markers
PWLists Pathways with Corresponding Gene Markers -
Compiled by Mike Palazzolo and Jim Wang from
CHDI
SCsLists Stem Cell-Related Genes with Corresponding Gene
Markers
TOMplot Graphical representation of the Topological
Overlap Matrix
TOMsimilarity Topological overlap matrix similarity and
dissimilarity
TOMsimilarityFromExpr Topological overlap matrix
TrueTrait Estimate the true trait underlying a list of
surrogate markers.
accuracyMeasures Accuracy measures for a 2x2 confusion matrix or
for vectors of predicted and observed values.
addErrorBars Add error bars to a barplot.
addGrid Add grid lines to an existing plot.
addGuideLines Add vertical "guide lines" to a dendrogram plot
addTraitToMEs Add trait information to multi-set module
eigengene structure
adjacency Calculate network adjacency
adjacency.polyReg Adjacency matrix based on polynomial regression
adjacency.splineReg Calculate network adjacency based on natural
cubic spline regression
alignExpr Align expression data with given vector
allocateJobs Divide tasks among workers
allowWGCNAThreads Allow and disable multi-threading for certain
WGCNA calculations
automaticNetworkScreening
One-step automatic network gene screening
automaticNetworkScreeningGS
One-step automatic network gene screening with
external gene significance
bicor Biweight Midcorrelation
bicorAndPvalue Calculation of biweight midcorrelations and
associated p-values
bicovWeights Weights used in biweight midcovariance
binarizeCategoricalColumns
Turn categorical columns into sets of binary
indicators
binarizeCategoricalVariable
Turn a categorical variable into a set of
binary indicators
blockSize Attempt to calculate an appropriate block size
to maximize efficiency of block-wise
calcualtions.
blockwiseConsensusModules
Find consensus modules across several datasets.
blockwiseIndividualTOMs
Calculation of block-wise topological overlaps
blockwiseModules Automatic network construction and module
detection
blueWhiteRed Blue-white-red color sequence
branchEigengeneDissim Branch dissimilarity based on eigennodes
(eigengenes).
branchSplit Branch split.
branchSplit.dissim Branch split based on dissimilarity.
branchSplitFromStabilityLabels
Branch split (dissimilarity) statistics derived
from labels determined from a stability study
checkAdjMat Check adjacency matrix
checkSets Check structure and retrieve sizes of a group
of datasets.
chooseOneHubInEachModule
Chooses a single hub gene in each module
chooseTopHubInEachModule
Chooses the top hub gene in each module
clusterCoef Clustering coefficient calculation
coClustering Co-clustering measure of cluster preservation
between two clusterings
coClustering.permutationTest
Permutation test for co-clustering
colQuantileC Fast colunm- and row-wise quantile of a matrix.
collapseRows Select one representative row per group
collapseRowsUsingKME Selects one representative row per group based
on kME
collectGarbage Iterative garbage collection.
conformityBasedNetworkConcepts
Calculation of conformity-based network
concepts.
conformityDecomposition
Conformity and module based decomposition of a
network adjacency matrix.
consensusCalculation Calculation of a (single) consenus with
optional data calibration.
consensusDissTOMandTree
Consensus clustering based on topological
overlap and hierarchical clustering
consensusKME Calculate consensus kME (eigengene-based
connectivities) across multiple data sets.
consensusMEDissimilarity
Consensus dissimilarity of module eigengenes.
consensusOrderMEs Put close eigenvectors next to each other in
several sets.
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering
of expression data
consensusRepresentatives
Consensus selection of group representatives
consensusTOM Consensus network (topological overlap).
consensusTreeInputs Get all elementary inputs in a consensus tree
convertNumericColumnsToNumeric
Convert character columns that represent
numbers to numeric
cor Fast calculations of Pearson correlation.
corAndPvalue Calculation of correlations and associated
p-values
corPredictionSuccess Qunatification of success of gene screening
corPvalueFisher Fisher's asymptotic p-value for correlation
corPvalueStudent Student asymptotic p-value for correlation
correlationPreservation
Preservation of eigengene correlations
coxRegressionResiduals
Deviance- and martingale residuals from a Cox
regression model
cutreeStatic Constant-height tree cut
cutreeStaticColor Constant height tree cut using color labels
displayColors Show colors used to label modules
dynamicMergeCut Threshold for module merging
empiricalBayesLM Empirical Bayes-moderated adjustment for
unwanted covariates
exportNetworkToCytoscape
Export network to Cytoscape
exportNetworkToVisANT Export network data in format readable by
VisANT
factorizeNonNumericColumns
Turn non-numeric columns into factors
fixDataStructure Put single-set data into a form useful for
multiset calculations.
formatLabels Break long character strings into multiple
lines
fundamentalNetworkConcepts
Calculation of fundamental network concepts
from an adjacency matrix.
goodGenes Filter genes with too many missing entries
goodGenesMS Filter genes with too many missing entries
across multiple sets
goodSamples Filter samples with too many missing entries
goodSamplesGenes Iterative filtering of samples and genes with
too many missing entries
goodSamplesGenesMS Iterative filtering of samples and genes with
too many missing entries across multiple data
sets
goodSamplesMS Filter samples with too many missing entries
across multiple data sets
greenBlackRed Green-black-red color sequence
greenWhiteRed Green-white-red color sequence
hierarchicalConsensusCalculation
Hierarchical consensus calculation
hierarchicalConsensusKME
Calculation of measures of fuzzy module
membership (KME) in hierarchical consensus
modules
hierarchicalConsensusMEDissimilarity
Hierarchical consensus calculation of module
eigengene dissimilarity
hierarchicalConsensusModules
Hierarchical consensus network construction and
module identification
hierarchicalConsensusTOM
Calculation of hierarchical consensus
topological overlap matrix
hierarchicalMergeCloseModules
Merge close (similar) hierarchical consensus
modules
hubGeneSignificance Hubgene significance
imputeByModule Impute missing data separately in each module
individualTOMs Calculate individual correlation network
matrices
initProgInd Inline display of progress
intramodularConnectivity
Calculation of intramodular connectivity
isMultiData Determine whether the supplied object is a
valid multiData structure
kMEcomparisonScatterplot
Function to plot kME values between two
comparable data sets.
keepCommonProbes Keep probes that are shared among given data
sets
labelPoints Label scatterplot points
labeledBarplot Barplot with text or color labels.
labeledHeatmap Produce a labeled heatmap plot
labeledHeatmap.multiPage
Labeled heatmap divided into several separate
plots.
labels2colors Convert numerical labels to colors.
list2multiData Convert a list to a multiData structure and
vice-versa.
lowerTri2matrix Reconstruct a symmetric matrix from a distance
(lower-triangular) representation
matchLabels Relabel module labels to best match the given
reference labels
matrixToNetwork Construct a network from a matrix
mergeCloseModules Merge close modules in gene expression data
metaAnalysis Meta-analysis of binary and continuous
variables
metaZfunction Meta-analysis Z statistic
minWhichMin Fast joint calculation of row- or column-wise
minima and indices of minimum elements
moduleColor.getMEprefix
Get the prefix used to label module eigengenes.
moduleEigengenes Calculate module eigengenes.
moduleMergeUsingKME Merge modules and reassign genes using kME.
moduleNumber Fixed-height cut of a dendrogram.
modulePreservation Calculation of module preservation statistics
mtd.apply Apply a function to each set in a multiData
structure.
mtd.mapply Apply a function to elements of given multiData
structures.
mtd.rbindSelf Turn a multiData structure into a single matrix
or data frame.
mtd.setAttr Set attributes on each component of a multiData
structure
mtd.setColnames Get and set column names in a multiData
structure.
mtd.simplify If possible, simplify a multiData structure to
a 3-dimensional array.
mtd.subset Subset rows and columns in a multiData
structure
multiData Create a multiData structure.
multiData.eigengeneSignificance
Eigengene significance across multiple sets
multiGSub Analogs of grep(l) and (g)sub for multiple
patterns and relacements
multiSetMEs Calculate module eigengenes.
multiUnion Union and intersection of multiple sets
mutualInfoAdjacency Calculate weighted adjacency matrices based on
mutual information
nPresent Number of present data entries.
nSets Number of sets in a multi-set variable
nearestCentroidPredictor
Nearest centroid predictor
nearestNeighborConnectivity
Connectivity to a constant number of nearest
neighbors
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest
neighbors across multiple data sets
networkConcepts Calculations of network concepts
networkScreening Identification of genes related to a trait
networkScreeningGS Network gene screening with an external gene
significance measure
newBlockInformation Create a list holding information about
dividing data into blocks
newBlockwiseData Create, merge and expand BlockwiseData objects
newConsensusOptions Create a list holding consensus calculation
options.
newConsensusTree Create a new consensus tree
newCorrelationOptions Creates a list of correlation options.
newNetworkOptions Create a list of network construction arguments
(options).
normalizeLabels Transform numerical labels into normal order.
numbers2colors Color representation for a numeric variable
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and
reflections.
orderMEs Put close eigenvectors next to each other
orderMEsByHierarchicalConsensus
Order module eigengenes by their hierarchical
consensus similarity
overlapTable Calculate overlap of modules
overlapTableUsingKME Determines significant overlap between modules
in two networks based on kME tables.
pickHardThreshold Analysis of scale free topology for
hard-thresholding.
pickSoftThreshold Analysis of scale free topology for
soft-thresholding
plotClusterTreeSamples
Annotated clustering dendrogram of microarray
samples
plotColorUnderTree Plot color rows in a given order, for example
under a dendrogram
plotCor Red and Green Color Image of Correlation Matrix
plotDendroAndColors Dendrogram plot with color annotation of
objects
plotEigengeneNetworks Eigengene network plot
plotMEpairs Pairwise scatterplots of eigengenes
plotMat Red and Green Color Image of Data Matrix
plotModuleSignificance
Barplot of module significance
plotMultiHist Plot multiple histograms in a single plot
plotNetworkHeatmap Network heatmap plot
populationMeansInAdmixture
Estimate the population-specific mean values in
an admixed population.
pquantile Parallel quantile, median, mean
prepComma Prepend a comma to a non-empty string
prependZeros Pad numbers with leading zeros to specified
total width
preservationNetworkConnectivity
Network preservation calculations
projectiveKMeans Projective K-means (pre-)clustering of
expression data
propVarExplained Proportion of variance explained by eigengenes.
proportionsInAdmixture
Estimate the proportion of pure populations in
an admixed population based on marker
expression values.
pruneAndMergeConsensusModules
Iterative pruning and merging of (hierarchical)
consensus modules
pruneConsensusModules Prune (hierarchical) consensus modules by
removing genes with low eigengene-based
intramodular connectivity
qvalue Estimate the q-values for a given set of
p-values
qvalue.restricted qvalue convenience wrapper
randIndex Rand index of two partitions
rankPvalue Estimate the p-value for ranking consistently
high (or low) on multiple lists
recutBlockwiseTrees Repeat blockwise module detection from
pre-calculated data
recutConsensusTrees Repeat blockwise consensus module detection
from pre-calculated data
redWhiteGreen Red-white-green color sequence
relativeCorPredictionSuccess
Compare prediction success
removeGreyME Removes the grey eigengene from a given
collection of eigengenes.
removePrincipalComponents
Remove leading principal components from data
replaceMissing Replace missing values with a constant.
returnGeneSetsAsList Return pre-defined gene lists in several
biomedical categories.
rgcolors.func Red and Green Color Specification
sampledBlockwiseModules
Blockwise module identification in sampled data
sampledHierarchicalConsensusModules
Hierarchical consensus module identification in
sampled data
scaleFreeFitIndex Calculation of fitting statistics for
evaluating scale free topology fit.
scaleFreePlot Visual check of scale-free topology
selectFewestConsensusMissing
Select columns with the lowest consensus number
of missing data
setCorrelationPreservation
Summary correlation preservation measure
shortenStrings Shorten given character strings by truncating
at a suitable separator.
sigmoidAdjacencyFunction
Sigmoid-type adacency function.
signedKME Signed eigengene-based connectivity
signifNumeric Round numeric columns to given significant
digits.
signumAdjacencyFunction
Hard-thresholding adjacency function
simpleConsensusCalculation
Simple calculation of a single consenus
simpleHierarchicalConsensusCalculation
Simple hierarchical consensus calculation
simulateDatExpr Simulation of expression data
simulateDatExpr5Modules
Simplified simulation of expression data
simulateEigengeneNetwork
Simulate eigengene network from a causal model
simulateModule Simulate a gene co-expression module
simulateMultiExpr Simulate multi-set expression data
simulateSmallLayer Simulate small modules
sizeGrWindow Opens a graphics window with specified
dimensions
sizeRestrictedClusterMerge
Cluter merging with size restrictions
softConnectivity Calculates connectivity of a weighted network.
spaste Space-less paste
standardColors Colors this library uses for labeling modules.
standardScreeningBinaryTrait
Standard screening for binatry traits
standardScreeningCensoredTime
Standard Screening with regard to a Censored
Time Variable
standardScreeningNumericTrait
Standard screening for numeric traits
stdErr Standard error of the mean of a given vector.
stratifiedBarplot Bar plots of data across two splitting
parameters
subsetTOM Topological overlap for a subset of a whole set
of genes
swapTwoBranches Select, swap, or reflect branches in a
dendrogram.
transposeBigData Transpose a big matrix or data frame
unsignedAdjacency Calculation of unsigned adjacency
userListEnrichment Measure enrichment between inputted and
user-defined lists
vectorTOM Topological overlap for a subset of the whole
set of genes
vectorizeMatrix Turn a matrix into a vector of non-redundant
components
verboseBarplot Barplot with error bars, annotated by
Kruskal-Wallis or ANOVA p-value
verboseBoxplot Boxplot annotated by a Kruskal-Wallis p-value
verboseIplot Scatterplot with density
verboseScatterplot Scatterplot annotated by regression line and
p-value
votingLinearPredictor Voting linear predictor