memrobmatrix-class {clusterCons}

Class "memrobmatrix"

Description

Objects of class 'memrobmatrix' hold the full membership robustness matrix generated from analysis of a consensus matrix. This includes the calculations of membership robustness for all features (e.g. genes) for each cluster. This can be useful as it allows you to see what conritbution a particular feature (e.g. gene) is making to other clusters. This could resonably be thought of as a measure similar to 'fuzziness' i.e. partial cluster membership. If the value of the membership robustness for a feature is similar in many clusters then that is additional evidence that the feature is not easily placed in any cluster.

Objects from the Class

Objects can be created by calls of the form new("memrobmatrix", ...), although they are usually generated internally by the memrob function.

Slots

mrm:

Object of class "matrix" - this is the full membership robustness matrix itself and therefore has the same dimensions as the original data object used in the clustering

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 memrob function.

Examples

showClass("memrobmatrix")

#load cmr
data(testcmr);

#calculate membership robustness
mr <- memrob(testcmr$e1_kmeans_k3)

#get the full membership robustness matrix (matrix itself held in slot 'mrm')
mrm <- mr$resultmatrix@mrm;