blockwiseConsensusModules: Find consensus modules across several datasets.

View source: R/blockwiseModulesC.R

blockwiseConsensusModulesR Documentation

Find consensus modules across several datasets.

Description

Perform network construction and consensus module detection across several datasets.

Usage

blockwiseConsensusModules(
     multiExpr, 

     # Data checking options

     checkMissingData = TRUE,

     # Blocking options

     blocks = NULL, 
     maxBlockSize = 5000, 
     blockSizePenaltyPower = 5,
     nPreclusteringCenters = NULL,
     randomSeed = 54321,

     # TOM precalculation arguments, if available

     individualTOMInfo = NULL,
     useIndivTOMSubset = NULL,

     # Network construction arguments: correlation options

     corType = "pearson",
     maxPOutliers = 1,
     quickCor = 0,
     pearsonFallback = "individual", 
     cosineCorrelation = FALSE,

     # Adjacency function options

     power = 6, 
     networkType = "unsigned", 
     checkPower = TRUE,
     replaceMissingAdjacencies = FALSE,

     # Topological overlap options

     TOMType = "unsigned",
     TOMDenom = "min",
     suppressNegativeTOM = FALSE,

     # Save individual TOMs?

     saveIndividualTOMs = TRUE,
     individualTOMFileNames = "individualTOM-Set%s-Block%b.RData",

     # Consensus calculation options: network calibration

     networkCalibration = c("single quantile", "full quantile", "none"),

     # Simple quantile calibration options

     calibrationQuantile = 0.95,
     sampleForCalibration = TRUE, sampleForCalibrationFactor = 1000,
     getNetworkCalibrationSamples = FALSE,

     # Consensus definition

     consensusQuantile = 0,
     useMean = FALSE,
     setWeights = NULL,

     # Saving the consensus TOM

     saveConsensusTOMs = FALSE,
     consensusTOMFilePattern = "consensusTOM-block.%b.RData",

     # Internal handling of TOMs

     useDiskCache = TRUE, chunkSize = NULL,
     cacheBase = ".blockConsModsCache",
     cacheDir = ".",

     # Alternative consensus TOM input from a previous calculation 

     consensusTOMInfo = NULL,

     # Basic tree cut options 

     # Basic tree cut options 

     deepSplit = 2, 
     detectCutHeight = 0.995, minModuleSize = 20,
     checkMinModuleSize = TRUE,

     # Advanced tree cut opyions

     maxCoreScatter = NULL, minGap = NULL,
     maxAbsCoreScatter = NULL, minAbsGap = NULL,
     minSplitHeight = NULL, minAbsSplitHeight = NULL,
     useBranchEigennodeDissim = FALSE,
     minBranchEigennodeDissim = mergeCutHeight,
     stabilityLabels = NULL,
     minStabilityDissim = NULL,

     pamStage = TRUE,  pamRespectsDendro = TRUE,

     # Gene reassignment and trimming from a module, and module "significance" criteria

     reassignThresholdPS = 1e-4,
     trimmingConsensusQuantile = consensusQuantile,
     minCoreKME = 0.5, minCoreKMESize = minModuleSize/3,
     minKMEtoStay = 0.2,

     # Module eigengene calculation options

     impute = TRUE,
     trapErrors = FALSE,

     #Module merging options

     equalizeQuantilesForModuleMerging = FALSE,
     quantileSummaryForModuleMerging = "mean",
     mergeCutHeight = 0.15, 
     mergeConsensusQuantile = consensusQuantile,

     # Output options

     numericLabels = FALSE,

     # General options

     nThreads = 0,
     verbose = 2, indent = 0, ...)

Arguments

multiExpr

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.

checkMissingData

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

blocks

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.

maxBlockSize

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.

blockSizePenaltyPower

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.

nPreclusteringCenters

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.

randomSeed

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.

individualTOMInfo

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.

useIndivTOMSubset

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.

corType

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.

maxPOutliers

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.

quickCor

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

pearsonFallback

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.

cosineCorrelation

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.

power

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.

networkType

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

checkPower

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.

replaceMissingAdjacencies

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

TOMType

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.

TOMDenom

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.

suppressNegativeTOM

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

saveIndividualTOMs

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

individualTOMFileNames

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.

networkCalibration

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

calibrationQuantile

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

sampleForCalibration

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.

sampleForCalibrationFactor

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.

getNetworkCalibrationSamples

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

consensusQuantile

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

useMean

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

setWeights

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

saveConsensusTOMs

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

consensusTOMFilePattern

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.

useDiskCache

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.

chunkSize

network similarities are saved in smaller chunks of size chunkSize.

cacheBase

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.

cacheDir

character string containing the desired path for the cache files.

consensusTOMInfo

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.

deepSplit

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.

detectCutHeight

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

minModuleSize

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

checkMinModuleSize

logical: should sanity checks be performed on minModuleSize?

maxCoreScatter

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.

minGap

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

maxAbsCoreScatter

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.

minAbsGap

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

minSplitHeight

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.

minAbsSplitHeight

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.

useBranchEigennodeDissim

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

minBranchEigennodeDissim

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.

stabilityLabels

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.

minStabilityDissim

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.

pamStage

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

pamRespectsDendro

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.

reassignThresholdPS

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

trimmingConsensusQuantile

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

minCoreKME

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).

minCoreKMESize

see minCoreKME above.

minKMEtoStay

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

impute

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

trapErrors

logical: should errors in calculations be trapped?

equalizeQuantilesForModuleMerging

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.

quantileSummaryForModuleMerging

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.

mergeCutHeight

dendrogram cut height for module merging.

mergeConsensusQuantile

consensus quantile for module merging. See mergeCloseModules for details.

numericLabels

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

nThreads

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.

verbose

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

indent

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.

Details

The function starts by optionally filtering out samples that have too many missing entries and genes that have either too many missing entries or zero variance in at least one set. Genes that are filtered out are left unassigned by the module detection. Returned eigengenes will contain NA in entries corresponding to filtered-out samples.

If blocks is not given and the number of genes exceeds maxBlockSize, genes are pre-clustered into blocks using the function consensusProjectiveKMeans; otherwise all genes are treated in a single block.

For each block of genes, the network is constructed and (if requested) topological overlap is calculated in each set. To minimize memory usage, calculated topological overlaps are optionally saved to disk in chunks until they are needed again for the calculation of the consensus network topological overlap.

Before calculation of the consensus Topological Overlap, individual TOMs are optionally calibrated. Calibration methods include single quantile scaling and full quantile normalization.

Single quantile scaling raises individual TOM in sets 2,3,... to a power such that the quantiles given by calibrationQuantile agree with the quantile in set 1. Since the high TOMs are usually the most important for module identification, the value of calibrationQuantile is close to (but not equal) 1. To speed up quantile calculation, the quantiles can be determined on a randomly-chosen component subset of the TOM matrices.

Full quantile normalization, implemented in normalize.quantiles, adjusts the TOM matrices such that all quantiles equal each other (and equal to the quantiles of the component-wise average of the individual TOM matrices).

Note that network calibration is performed separately in each block, i.e., the normalizing transformation may differ between blocks. This is necessary to avoid manipulating a full TOM in memory.

The consensus TOM is calculated as the component-wise consensusQuantile quantile of the individual (set) TOMs; that is, for each gene pair (TOM entry), the consensusQuantile quantile across all input sets. Alternatively, one can also use (weighted) component-wise mean across all imput data sets. If requested, the consensus topological overlaps are saved to disk for later use.

Genes are then clustered using average linkage hierarchical clustering and modules are identified in the resulting dendrogram by the Dynamic Hybrid tree cut. Found modules are trimmed of genes whose consensus module membership kME (that is, correlation with module eigengene) is less than minKMEtoStay. Modules in which fewer than minCoreKMESize genes have consensus KME higher than minCoreKME are disbanded, i.e., their constituent genes are pronounced unassigned.

After all blocks have been processed, the function checks whether there are genes whose KME in the module they assigned is lower than KME to another module. If p-values of the higher correlations are smaller than those of the native module by the factor reassignThresholdPS (in every set), the gene is re-assigned to the closer module.

In the last step, modules whose eigengenes are highly correlated are merged. This is achieved by clustering module eigengenes using the dissimilarity given by one minus their correlation, cutting the dendrogram at the height mergeCutHeight and merging all modules on each branch. The process is iterated until no modules are merged. See mergeCloseModules for more details on module merging.

The argument quick specifies the precision of handling of missing data in the correlation calculations. Zero will cause all calculations to be executed precisely, which may be significantly slower than calculations without missing data. Progressively higher values will speed up the calculations but introduce progressively larger errors. Without missing data, all column means and variances can be pre-calculated before the covariances are calculated. When missing data are present, exact calculations require the column means and variances to be calculated for each covariance. The approximate calculation uses the pre-calculated mean and variance and simply ignores missing data in the covariance calculation. If the number of missing data is high, the pre-calculated means and variances may be very different from the actual ones, thus potentially introducing large errors. The quick value times the number of rows specifies the maximum difference in the number of missing entries for mean and variance calculations on the one hand and covariance on the other hand that will be tolerated before a recalculation is triggered. The hope is that if only a few missing data are treated approximately, the error introduced will be small but the potential speedup can be significant.

Value

A list with the following components:

colors

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.

unmergedColors

module colors or numeric labels before the module merging step.

multiMEs

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.

goodSamples

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.

goodGenes

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

dendrograms

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.

TOMFiles

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.

blockGenes

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.

blocks

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.

blockOrder

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.

originCount

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.

networkCalibrationSamples

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.)

Note

If the input datasets have large numbers of genes, consider carefully the maxBlockSize as it significantly affects the memory footprint (and whether the function will fail with a memory allocation error). From a theoretical point of view it is advantageous to use blocks as large as possible; on the other hand, using smaller blocks is substantially faster and often the only way to work with large numbers of genes. As a rough guide, it is unlikely a standard desktop computer with 4GB memory or less will be able to work with blocks larger than 7000 genes.

Author(s)

Peter Langfelder

References

Langfelder P, Horvath S (2007) Eigengene networks for studying the relationships between co-expression modules. BMC Systems Biology 2007, 1:54

See Also

goodSamplesGenesMS for basic quality control and filtering;

adjacency, TOMsimilarity for network construction;

hclust for hierarchical clustering;

cutreeDynamic for adaptive branch cutting in hierarchical clustering dendrograms;

mergeCloseModules for merging of close modules.


WGCNA documentation built on April 23, 2022, 1:06 a.m.