Reorder given (eigen-)vectors such that similar ones (as measured by correlation) are next to each other.
orderMEs(MEs, greyLast = TRUE,
greyName = paste(moduleColor.getMEprefix(), "grey", sep=""),
orderBy = 1, order = NULL,
useSets = NULL, verbose = 0, indent = 0)A vector of lists of the same type as MEs containing the re-ordered eigengenes.
Module eigengenes in a multi-set format (see checkSets). A vector of lists,
with each list corresponding to one dataset and the module eigengenes in the component data,
that is MEs[[set]]$data[sample, module] is the expression of the eigengene of module module
in sample
sample in dataset set. The number of samples can be different between the sets, but the
modules must be the same.
Normally the color grey is reserved for unassigned genes; hence the grey module is not
a proper module and it is conventional to put it last. If this is not desired, set the parameter to
FALSE.
Name of the grey module eigengene.
Specifies the set by which the eigengenes are to be ordered (in all other sets as well).
Defaults to the first set in useSets (or the first set, if useSets is not given).
Allows the user to specify a custom ordering.
Allows the user to specify for which sets the eigengene ordering is to be performed.
Controls verbostity of printed progress messages. 0 means silent, nonzero verbose.
A single non-negative integer controling indentation of printed messages. 0 means no indentation, each unit above zero adds two spaces.
Peter Langfelder, Peter.Langfelder@gmail.com
Ordering module eigengenes is useful for plotting purposes. For this function the order can be specified explicitly, or a set can be given in which the correlations of the eigengenes will determine the order. For the latter, a hierarchical dendrogram is calculated and the order given by the dendrogram is used for the eigengenes in all other sets.
moduleEigengenes, multiSetMEs, consensusOrderMEs