Package 'WGCNA' - Laboratory Web Sites - UCLA

18 blockwiseConsensusModules
Value
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.
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
goodSamples
goodGenes
module eigengenes corresponding to the modules returned in colors, in multiset
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.
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
blockGenes
blocks
if saveTOMs==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