WGCNA: orderMEs – R documentation

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WGCNA

orderMEs

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, Peter.Langfelder@gmail.com