Main functions

cluscomp - generate consensus matrices from re-sampled clustering experiments with the option of multiple algorithms and parameters
clrob - calculate the robustness of the clusters from the consensus matrix
memrob - calculate the cluster membership robustness from the consensus matrix

Algorithms - Internal functions to call the individual clustering algorithms

agnes_clmem - wrapper for the agnes function of package cluster
diana_clmem - wrapper for the diana function of package cluster
hclust_clmem - wrapper for the hclust function of package cluster
kmeans_clmem - wrapper for the kmeans function of package cluster
pam_clmem - wrapper for the pam function of package cluster
apcluster_clmem - wrapper for the apclusterK function of package apcluster

Analysis curves - Functions to calculate AUC related metrics

auc - calculates the area under the curve for a series of clustering experiments with the same cluster number
aucs - calculates the areas under the curves of a series of clustering experiments over a range of cluster numbers
deltak - calculates the change in the area under the curve


Plotting - plotting methods
 
aucplot - plot the areas under the curves from an AUC object (typically produced by the aucs() function)
dkplot - plot the delta-K curve to estimate the optimal cluster number (k) from a dk object (typically produced by the deltak() function)
expressionPlot - plot the original data partitioned by cluster membership
membBoxPlot - plot a box and whisker plot of the membership robustness for each cluster

Data checking and class definition - Functions to check data and object validity

data_check - check that the provided data.frame is formatted correctly
expSetProcess - extracts the data set from an object of class expressionSet  
validConsMatrixObject - check the validity of a consmatrix object
validMergeMatrixObject - check the validity of a mergematrix object
validMemRobListObject - check the validity of a membership robustness list object
validMemRobMatrixObject - check the validity of a membership robustness matrix object
validAUCObject - check the validity of an AUC calculation object
validDkObject - check the validity of a delta-K calculation object

Data - provided data sets
golub - leukemia microarray datasets for AML and ALL patients       
sim_class - simulated gene expression data for classes
sim_profile - simlulated gene expression profiles
testcmr - an example cluscomp result to test out downstream functionality