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clusterCons - a package for consensus clustering in R

Calculate the Consensus Clustering Result from Re-Sampled Clustering Experiments with the Option of Using Multiple Algorithms and Parameters

Description

clusterCons contains functions for the calculation of robustness measures for clusters and cluster membership based on consensus matrices generated from bootstrapped clustering experiments in which a random proportion of rows of the data set are used in each individual clustering. This allows the user to prioritise clusters and the members of clusters based on their consistency in this regime.

The functions allow the user to select several algorithms to use in the re-sampling scheme and with any of the parameters that the algorithm would normally take.

Installation

The package can be installed from either .tar.gz (*nix) or .ZIP (windows) executables via the release on the right hand side of this web-page. These can be installed using the usual methods for R package installation either at the command line or within R.

clusterCons has recently been updated to be compatible with R version 4.1.2 and will soon re-appear on the CRAN repository after an absence of a few years. We will update this page as soon as it is available.

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Version

Install

install.packages('clusterCons')

Monthly Downloads

83

Version

1.2

License

GPL (> 2)

Issues

0

Pull Requests

0

Stars

1

Forks

0

Maintainer

Dr. T. Ian Simpson

Last Published

February 22nd, 2022

Functions in clusterCons (1.2)

consmatrix-class

Class "consmatrix"
checks

Functions to check the integrity of various objects
clrob

Calculate the cluster robustness from consensus clustering results
cluscomp

Perform consensus clustering with the option of using multiple algorithms and parameters and merging
deltak

Function to calculate the change in the area under the curve (AUC) across a range of cluster number values
clusterCons-package

Calculate consensus clustering results from re-sampled clustering experiments with the option of using multiple algorithms and parameters
data

Data sets for the clusterCons package
aucplot

Generate an area under the curve plot using lattice graphics
memroblist-class

Class "memroblist"
memrobmatrix-class

Class "memrobmatrix"
dk-class

Class "dk"
auc-class

Class "auc"
wrappers

Functions to wrap command calls to clustering functions
mergematrix-class

Class "mergematrix"
dkplot

Generate a delta-K plot from area under the curve (AUC) values across multiple cluster numbers.
expSetProcess

Internal function to extract the data from an expressionSet class object from the affy package for use with cluscomp
membBoxPlot

Generate a box and whisker plot of membership robustness for all clusters
auc

Calculate area under the curve statistics
expressionPlot

Generate a profile plot for the data partitioned by cluster membership.
memrob

Calculate the membership robustness from consensus clustering results