orderMEs: Put close eigenvectors next to each other

In WGCNA: Weighted Correlation Network Analysis

Put close eigenvectors next to each other

Description

Reorder given (eigen-)vectors such that similar ones (as measured by correlation) are next to each other.

Usage

orderMEs(MEs, greyLast = TRUE, 
         greyName = paste(moduleColor.getMEprefix(), "grey", sep=""), 
         orderBy = 1, order = NULL, 
         useSets = NULL,  verbose = 0, indent = 0)

Arguments

MEs	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.
greyLast	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.
greyName	Name of the grey module eigengene.
orderBy	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).
order	Allows the user to specify a custom ordering.
useSets	Allows the user to specify for which sets the eigengene ordering is to be performed.
verbose	Controls verbostity of printed progress messages. 0 means silent, nonzero verbose.
indent	A single non-negative integer controling indentation of printed messages. 0 means no indentation, each unit above zero adds two spaces.

Details

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.

Value

A vector of lists of the same type as MEs containing the re-ordered eigengenes.

Author(s)

Peter Langfelder, [e-mail]

See Also

moduleEigengenes, multiSetMEs, consensusOrderMEs

WGCNA documentation built on Sept. 18, 2024, 5:08 p.m.