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NMF (version 0.28)

consensushc: Hierarchical Clustering of a Consensus Matrix

Description

The function consensushc computes the hierarchical clustering of a consensus matrix, using the matrix itself as a similarity matrix and average linkage. It is

Usage

consensushc(object, ...)

# S4 method for matrix consensushc(object, method = "average", dendrogram = TRUE)

# S4 method for NMFfitX consensushc(object, what = c("consensus", "fit"), ...)

Value

an object of class dendrogram or hclust

depending on the value of argument dendrogram.

Arguments

object

a matrix or an NMFfitX object, as returned by multiple NMF runs.

...

extra arguments passed to next method calls

method

linkage method passed to hclust.

dendrogram

a logical that specifies if the result of the hierarchical clustering (en hclust object) should be converted into a dendrogram. Default value is TRUE.

what

character string that indicates which matrix to use in the computation.

Methods

consensushc

signature(object = "matrix"): Workhorse method for matrices.

consensushc

signature(object = "NMF"): Compute the hierarchical clustering on the connectivity matrix of object.

consensushc

signature(object = "NMFfitX"): Compute the hierarchical clustering on the consensus matrix of object, or on the connectivity matrix of the best fit in object.