mergematrix-class: Class "mergematrix"

In clusterCons: Consensus Clustering using Multiple Algorithms and Parameters

Class "mergematrix"

Description

Objects of class 'mergematrix' hold the merge matrix in the same way that a consmatrix object holds a consensus matrix. As merge matrices only make sense in the context of the consensus clustering results that were used to generate them we do not store the meta-data for any one consensus clustering parameter set as we do for a 'consmatrix' object. All we need to identify the 'mergematrix' is the cluster number.

Objects from the Class

Objects can be created by calls of the form new("mergematrix", ...), although they are normally generated by the cluscomp function when merge is specfied.

Slots

cm:

Object of class "matrix" - the merge matrix itself

k:

Object of class "numeric" - the cluster number (k) value for which the merge was calculated

a:

Object of class "character" - always takes the value of 'merge' to identify it as a merge matrix

Author(s)

Dr. T. Ian Simpson [e-mail]

References

Merged consensus clustering to assess and improve class discovery with microarray data. Simpson TI, Armstrong JD and Jarman AP. BMC Bioinformatics 2010, 11:590.

See Also

Also see the cluscomp function.

Examples

showClass("mergematrix")

#load the cmr
data(testcmr);

#get a merge matrix object
mm <- testcmr$merge_k4;

#plot a heatmap of the merge matrix
heatmap(mm@cm);

clusterCons documentation built on March 18, 2022, 5:16 p.m.