orderMEsByHierarchicalConsensus: Order module eigengenes by their hierarchical consensus...

In WGCNA: Weighted Correlation Network Analysis

Order module eigengenes by their hierarchical consensus similarity

Description

This function calculates a hiearchical consensus similarity of the input eigengenes, clusters the eigengenes according to the similarity and returns the input module eigengenes ordered by the order of resulting dendrogram.

Usage

orderMEsByHierarchicalConsensus(
    MEs, 
    networkOptions, 
    consensusTree, 
    greyName = "ME0", 
    calibrate = FALSE)

Arguments

MEs	Module eigengenes, or more generally, vectors, to be ordered, in a multiData format: A vector of lists, one per set. Each set must contain a component data that contains the module eigenegens or general vectors, with rows corresponding to samples and columns to genes or probes.
networkOptions	A single list of class NetworkOptions giving options for network calculation for all of the networks, or a multiData structure containing one such list for each input data set.
consensusTree	A list specifying the consensus calculation. See newConsensusTree for details.
greyName	Specifies the column name of eigengene of the "module" that contains unassigned genes. This eigengene (column) will be excluded from the clustering and will be put last in the order.
calibrate	Logical: should module eigengene similarities be calibrated? This setting overrides the calibration options in consensusTree.

Value

A multiData structure of the same format as the input MEs, with columns ordered by the calculated dendrogram.

Author(s)

Peter Langfelder

See Also

hierarchicalConsensusMEDissimilarity for calculating the consensus ME dissimilarity

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