consensusOrderMEs: Put close eigenvectors next to each other in several sets.

View source: R/Functions.R

consensusOrderMEsR Documentation

Put close eigenvectors next to each other in several sets.

Description

Reorder given (eigen-)vectors such that similar ones (as measured by correlation) are next to each other. This is a multi-set version of orderMEs; the dissimilarity used can be of consensus type (for each pair of eigenvectors the consensus dissimilarity is the maximum of individual set dissimilarities over all sets) or of majority type (for each pair of eigenvectors the consensus dissimilarity is the average of individual set dissimilarities over all sets).

Usage

consensusOrderMEs(MEs, useAbs = FALSE, useSets = NULL, 
                  greyLast = TRUE, 
                  greyName = paste(moduleColor.getMEprefix(), "grey", sep=""), 
                  method = "consensus")

Arguments

MEs

Module eigengenes of several sets 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.

useAbs

Controls whether vector similarity should be given by absolute value of correlation or plain correlation.

useSets

Allows the user to specify for which sets the eigengene ordering is to be performed.

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.

method

A character string giving the method to be used calculating the consensus dissimilarity. Allowed values are (abbreviations of) "consensus" and "majority". The consensus dissimilarity is calculated as the maximum of given set dissimilarities for "consensus" and as the average for "majority".

Details

Ordering module eigengenes is useful for plotting purposes. This function calculates the consensus or majority dissimilarity of given eigengenes over the sets specified by useSets (defaults to all sets). A hierarchical dendrogram is calculated using the dissimilarity 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

See Also

moduleEigengenes, multiSetMEs, orderMEs


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