NMF: consensushc – R documentation

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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 signature 'matrix'
consensushc(object,
    method = "average", dendrogram = TRUE)

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

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.

Value

an object of class dendrogram or hclust depending on the value of argument dendrogram.

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.

NMF

Algorithms and Framework for Nonnegative Matrix Factorization (NMF)

v0.23.0

GPL (>= 2)

Authors

Renaud Gaujoux, Cathal Seoighe

Initial release

2020-07-30