WGCNA: orderMEsByHierarchicalConsensus – R documentation

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orderMEsByHierarchicalConsensus

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

orderMEsByHierarchicalConsensus

Description

Usage

Arguments

Value

Author(s)

See Also

WGCNA

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