ADC: Aggregated data clustering

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

Aggregated data clustering

Description

Aggregated Data Clustering (ADC) is a direct clustering multi-source technique. The data matrices are merged into a single fused data matrix on which a dissimilarity matrix is computed. Hierarchical clustering is then performed on this dissimilarity matrix.

Usage

ADC(
  List,
  distmeasure = "tanimoto",
  normalize = FALSE,
  method = NULL,
  clust = "agnes",
  linkage = "flexible",
  alpha = 0.625
)

Arguments

List	A list of data matrices of the same type. It is assumed the rows are corresponding with the objects.
distmeasure	Choice of metric for the dissimilarity matrix (character). Should be one of "tanimoto", "euclidean", "jaccard", "hamming". Defaults to "tanimoto".
normalize	Logical. Indicates whether to normalize the distance matrices or not, defaults to FALSE. This is recommended if different distance types are used. More details on normalization in Normalization.
method	A method of normalization. Should be one of "Quantile","Fisher-Yates", "standardize","Range" or any of the first letters of these names. Default is NULL.
clust	Choice of clustering function (character). Defaults to "agnes".
linkage	Choice of inter group dissimilarity (character). Defaults to "flexible".
alpha	The parameter alpha to be used in the "flexible" linkage of the agnes function. Defaults to 0.625 and is only used if the linkage is set to "flexible".

Value

The returned value is a list with the following three elements.

AllData	Fused data matrix of the data matrices
DistM	The resulting distance matrix
Clust	The resulting clustering

The value has class 'ADC'. The Clust element will be of interest for further applications.

References

Fodeh, S. J., Punch, W. & Tan, P.-N. (2013). On unifying multi-source information from probabilistically generated functional data. Proteins 81:1298-1310.

Examples

## Not run: 
data(mosaic_toy)
L <- mosaic_toy$List
res_ADC <- ADC(List=L, distmeasure="euclidean", normalize=FALSE, method=NULL,
               clust="agnes", linkage="flexible", alpha=0.625)

## End(Not run)

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