expression data in the multi-set format (see checkSets). A vector of lists, one per set. Each set must contain a component data that contains the expression data, with rows corresponding to samples and columns to genes or probes.

logical: should data be checked for excessive numbers of missing entries in genes and samples, and for genes with zero variance? See details.

optional specification of blocks in which hierarchical clustering and module detection should be performed. If given, must be a numeric vector with one entry per gene of multiExpr giving the number of the block to which the corresponding gene belongs.

integer giving maximum block size for module detection. Ignored if blocks above is non-NULL. Otherwise, if the number of genes in datExpr exceeds maxBlockSize, genes will be pre-clustered into blocks whose size should not exceed maxBlockSize.

number specifying how strongly blocks should be penalized for exceeding the maximum size. Set to a lrge number or Inf if not exceeding maximum block size is very important.

number of centers to be used in the preclustering. Defaults to smaller of nGenes/20 and 100*nGenes/maxBlockSize, where nGenes is the nunber of genes (variables) in multiExpr.

integer to be used as seed for the random number generator before the function starts. If a current seed exists, it is saved and restored upon exit. If NULL is given, the function will not save and restore the seed.

Optional data for TOM matrices in individual data sets. This object is returned by the function blockwiseIndividualTOMs. If not given, appropriate topological overlaps will be calculated using the network contruction options below.

If individualTOMInfo is given, this argument allows to only select a subset of the individual set networks contained in individualTOMInfo. It should be a numeric vector giving the indices of the individual sets to be used. Note that this argument is NOT applied to multiExpr.

character string specifying the correlation to be used. Allowed values are (unique abbreviations of) "pearson" and "bicor", corresponding to Pearson and bidweight midcorrelation, respectively. Missing values are handled using the pariwise.complete.obs option.

only used for corType=="bicor". Specifies the maximum percentile of data that can be considered outliers on either side of the median separately. For each side of the median, if higher percentile than maxPOutliers is considered an outlier by the weight function based on 9*mad(x), the width of the weight function is increased such that the percentile of outliers on that side of the median equals maxPOutliers. Using maxPOutliers=1 will effectively disable all weight function broadening; using maxPOutliers=0 will give results that are quite similar (but not equal to) Pearson correlation.

real number between 0 and 1 that controls the handling of missing data in the calculation of correlations. See details.

Specifies whether the bicor calculation, if used, should revert to Pearson when median absolute deviation (mad) is zero. Recongnized values are (abbreviations of) "none", "individual", "all". If set to "none", zero mad will result in NA for the corresponding correlation. If set to "individual", Pearson calculation will be used only for columns that have zero mad. If set to "all", the presence of a single zero mad will cause the whole variable to be treated in Pearson correlation manner (as if the corresponding robust option was set to FALSE). Has no effect for Pearson correlation. See bicor.

logical: should the cosine version of the correlation calculation be used? The cosine calculation differs from the standard one in that it does not subtract the mean.

soft-thresholding power for network construction. Either a single number or a vector of the same length as the number of sets, with one power for each set.

network type. Allowed values are (unique abbreviations of) "unsigned", "signed", "signed hybrid". See adjacency.

logical: should basic sanity check be performed on the supplied power? If you would like to experiment with unusual powers, set the argument to FALSE and proceed with caution.

logical: should missing values in the calculation of adjacency be replaced by 0?

one of "none", "unsigned", "signed", "signed Nowick", "unsigned 2", "signed 2" and "signed Nowick 2". If "none", adjacency will be used for clustering. See TOMsimilarityFromExpr for details.

a character string specifying the TOM variant to be used. Recognized values are "min" giving the standard TOM described in Zhang and Horvath (2005), and "mean" in which the min function in the denominator is replaced by mean. The "mean" may produce better results but at this time should be considered experimental.

Logical: should the result be set to zero when negative? Negative TOM values can occur when TOMType is "signed Nowick".

logical: should individual TOMs be saved to disk for later use?

character string giving the file names to save individual TOMs into. The following tags should be used to make the file names unique for each set and block: %s will be replaced by the set number; %N will be replaced by the set name (taken from names(multiExpr)) if it exists, otherwise by set number; %b will be replaced by the block number. If the file names turn out to be non-unique, an error will be generated.

network calibration method. One of "single quantile", "full quantile", "none" (or a unique abbreviation of one of them).

if networkCalibration is "single quantile", topological overlaps (or adjacencies if TOMs are not computed) will be scaled such that their calibrationQuantile quantiles will agree.

if TRUE, calibration quantiles will be determined from a sample of network similarities. Note that using all data can double the memory footprint of the function and the function may fail.

determines the number of samples for calibration: the number is 1/calibrationQuantile * sampleForCalibrationFactor. Should be set well above 1 to ensure accuracy of the sampled quantile.

logical: should samples used for TOM calibration be saved for future analysis? This option is only available when sampleForCalibration is TRUE.

quantile at which consensus is to be defined. See details.

logical: should the consensus be determined from a (possibly weighted) mean across the data sets rather than a quantile?

Optional vector (one component per input set) of weights to be used for weighted mean consensus. Only used when useMean above is TRUE.

logical: should the consensus topological overlap matrices for each block be saved and returned?

character string containing the file namefiles containing the consensus topological overlaps. The tag %b will be replaced by the block number. If the resulting file names are non-unique (for example, because the user gives a file name without a %b tag), an error will be generated. These files are standard R data files and can be loaded using the load function.

should calculated network similarities in individual sets be temporarilly saved to disk? Saving to disk is somewhat slower than keeping all data in memory, but for large blocks and/or many sets the memory footprint may be too big.

network similarities are saved in smaller chunks of size chunkSize.

character string containing the desired name for the cache files. The actual file names will consists of cacheBase and a suffix to make the file names unique.

character string containing the desired path for the cache files.

optional list summarizing consensus TOM, output of consensusTOM. It contains information about pre-calculated consensus TOM. Supplying this argument replaces TOM calculation, so none of the individual or consensus TOM calculation arguments are taken into account.

integer value between 0 and 4. Provides a simplified control over how sensitive module detection should be to module splitting, with 0 least and 4 most sensitive. See cutreeDynamic for more details.

dendrogram cut height for module detection. See cutreeDynamic for more details.

minimum module size for module detection. See cutreeDynamic for more details.

logical: should sanity checks be performed on minModuleSize?

maximum scatter of the core for a branch to be a cluster, given as the fraction of cutHeight relative to the 5th percentile of joining heights. See cutreeDynamic for more details.

minimum cluster gap given as the fraction of the difference between cutHeight and the 5th percentile of joining heights. See cutreeDynamic for more details.

maximum scatter of the core for a branch to be a cluster given as absolute heights. If given, overrides maxCoreScatter. See cutreeDynamic for more details.

minimum cluster gap given as absolute height difference. If given, overrides minGap. See cutreeDynamic for more details.

Minimum split height given as the fraction of the difference between cutHeight and the 5th percentile of joining heights. Branches merging below this height will automatically be merged. Defaults to zero but is used only if minAbsSplitHeight below is NULL.

Minimum split height given as an absolute height. Branches merging below this height will automatically be merged. If not given (default), will be determined from minSplitHeight above.

Logical: should branch eigennode (eigengene) dissimilarity be considered when merging branches in Dynamic Tree Cut?

Minimum consensus branch eigennode (eigengene) dissimilarity for branches to be considerd separate. The branch eigennode dissimilarity in individual sets is simly 1-correlation of the eigennodes; the consensus is defined as quantile with probability consensusQuantile.

Optional matrix of cluster labels that are to be used for calculating branch dissimilarity based on split stability. The number of rows must equal the number of genes in multiExpr; the number of columns (clusterings) is arbitrary. See branchSplitFromStabilityLabels for details.

Minimum stability dissimilarity criterion for two branches to be considered separate. Should be a number between 0 (essentially no dissimilarity required) and 1 (perfect dissimilarity or distinguishability based on stabilityLabels). See branchSplitFromStabilityLabels for details.

logical. If TRUE, the second (PAM-like) stage of module detection will be performed. See cutreeDynamic for more details.

Logical, only used when pamStage is TRUE. If TRUE, the PAM stage will respect the dendrogram in the sense an object can be PAM-assigned only to clusters that lie below it on the branch that the object is merged into. See cutreeDynamic for more details.

per-set p-value ratio threshold for reassigning genes between modules. See Details.

a number between 0 and 1 specifying the consensus quantile used for kME calculation that determines module trimming according to the arguments below.

a number between 0 and 1. If a detected module does not have at least minModuleKMESize genes with eigengene connectivity at least minCoreKME, the module is disbanded (its genes are unlabeled and returned to the pool of genes waiting for mofule detection).

see minCoreKME above.

genes whose eigengene connectivity to their module eigengene is lower than minKMEtoStay are removed from the module.

logical: should imputation be used for module eigengene calculation? See moduleEigengenes for more details.

logical: should errors in calculations be trapped?

Logical: equalize quantiles of the module eigengene networks before module merging? If TRUE, the quantiles of the eigengene correlation matrices (interpreted as a single vectors of non-redundant components) will be equalized across the input data sets. Note that although this seems like a reasonable option, it should be considered experimental and not necessarily recommended.

One of "mean" or "median". If quantile equalization of the module eigengene networks is performed, the resulting "normal" quantiles will be given by this function of the corresponding quantiles across the input data sets.

dendrogram cut height for module merging.

consensus quantile for module merging. See mergeCloseModules for details.

logical: should the returned modules be labeled by colors (FALSE), or by numbers (TRUE)?

non-negative integer specifying the number of parallel threads to be used by certain parts of correlation calculations. This option only has an effect on systems on which a POSIX thread library is available (which currently includes Linux and Mac OSX, but excludes Windows). If zero, the number of online processors will be used if it can be determined dynamically, otherwise correlation calculations will use 2 threads.

integer level of verbosity. Zero means silent, higher values make the output progressively more and more verbose.

indentation for diagnostic messages. Zero means no indentation, each unit adds two spaces.

Other arguments. At present these can include reproduceBranchEigennodeQuantileError that instructs the function to reproduce a bug in branch eigennode dissimilarity calculations for purposes if reproducing old reults.

module assignment of all input genes. A vector containing either character strings with module colors (if input numericLabels was unset) or numeric module labels (if numericLabels was set to TRUE). The color "grey" and the numeric label 0 are reserved for unassigned genes.

module colors or numeric labels before the module merging step.

module eigengenes corresponding to the modules returned in colors, in multi-set format. A vector of lists, one per set, containing eigengenes, proportion of variance explained and other information. See multiSetMEs for a detailed description.

a list, with one component per input set. Each component is a logical vector with one entry per sample from the corresponding set. The entry indicates whether the sample in the set passed basic quality control criteria.

a logical vector with one entry per input gene indicating whether the gene passed basic quality control criteria in all sets.

a list with one component for each block of genes. Each component is the hierarchical clustering dendrogram obtained by clustering the consensus gene dissimilarity in the corresponding block.

if saveConsensusTOMs==TRUE, a vector of character strings, one string per block, giving the file names of files (relative to current directory) in which blockwise topological overlaps were saved.

a list with one component for each block of genes. Each component is a vector giving the indices (relative to the input multiExpr) of genes in the corresponding block.

if input blocks was given, its copy; otherwise a vector of length equal number of genes giving the block label for each gene. Note that block labels are not necessarilly sorted in the order in which the blocks were processed (since we do not require this for the input blocks). See blockOrder below.

a vector giving the order in which blocks were processed and in which blockGenes above is returned. For example, blockOrder[1] contains the label of the first-processed block.

A vector of length nSets that contains, for each set, the number of (calibrated) elements that were less than or equal the consensus for that element.

if the input getNetworkCalibrationSamples is TRUE, this component is a list with one component per block. Each component is again a list with two components: sampleIndex contains indices of the distance structure in which TOM is stored that were sampled, and TOMSamples is a matrix whose rows correspond to TOM samples and columns to individual set. Hence, networkCalibrationSamples[[blockNo]]$TOMSamples[index, setNo] contains the TOM entry that corresponds to element networkCalibrationSamples[[blockNo]]$sampleIndex[index] of the TOM distance structure in block blockNo and set setNo. (For details on the distance structure, see dist.)