CompareSilCluster: Compares medoid clustering results based on silhouette widths

In MosaiClusteR: An Umbrella Framework for Multi-Source and Multi-Omics Clustering

Compares medoid clustering results based on silhouette widths

Description

The function CompareSilCluster compares the results of two medoid clusterings. The null hypothesis is that the clustering is identical. A test statistic is calculated and a p-value obtained with bootstrapping.

Usage

CompareSilCluster(
  List,
  type = c("data", "dist"),
  distmeasure = c("tanimoto", "tanimoto"),
  normalize = c(FALSE, FALSE),
  method = c(NULL, NULL),
  nrclusters = NULL,
  names = NULL,
  nboot = 100,
  plottype = "new",
  location = NULL
)

Arguments

List	A list of data matrices. It is assumed the rows are corresponding with the objects.
type	indicates whether the provided matrices in "List" are either data matrices or distance matrices. Type should be one of "data" or "dist".
distmeasure	A vector of the distance measures to be used on each data matrix. Defaults to c("tanimoto","tanimoto").
normalize	Logical. Indicates whether to normalize the distance matrices. Default is c(FALSE, FALSE).
method	A method of normalization. Default is c(NULL,NULL).
nrclusters	The number of clusters to cut the dendrogram in. Default is NULL.
names	The labels to give to the elements in List. Default is NULL.
nboot	Number of bootstraps to be run. Default is 100.
plottype	Should be one of "pdf","new" or "sweave". Default is "new".
location	If plottype is "pdf", a location should be provided here. Default is NULL.

Value

A plot of the density of the statistic under the null hypothesis. Further a list with two elements:

Observed Statistic	The observed statistical value
P-Value	The P-value of the obtained statistic retrieved after bootstrapping

.

Examples

## Not run: 
data(fingerprintMat)
data(targetMat)

List=list(fingerprintMat,targetMat)

Comparison=CompareSilCluster(List=List,type="data",
distmeasure=c("tanimoto","tanimoto"),normalize=c(FALSE,FALSE),method=c(NULL,NULL),
nrclusters=7,names=NULL,nboot=100,plottype="new",location=NULL)

Comparison

## End(Not run)

MosaiClusteR documentation built on Oct. 25, 2026, 1:08 a.m.