dist_matrix

Dispatch of amap::Dist, cosine_dist, and norm_inprod methods.

Density-based clustering methods are well adapted to the clustering of high-dimensional data and enable the discovery of core groups of various shapes despite large amounts of noise. This package provides a novel density-based cluster extraction method, OPTICS k-Xi, and a framework to compare k-Xi models using distance-based metrics to investigate datasets with unknown number of clusters. The vignette first introduces density-based algorithms with simulated datasets, then presents and evaluates the k-Xi cluster extraction method. Finally, the models comparison framework is described and experimented on 2 genetic datasets to identify groups and their discriminating features. The k-Xi algorithm is a novel OPTICS cluster extraction method that specifies directly the number of clusters and does not require fine-tuning of the steepness parameter as the OPTICS Xi method. Combined with a framework that compares models with varying parameters, the OPTICS k-Xi method can identify groups in noisy datasets with unknown number of clusters. Results on summarized genetic data of 1,200 patients are in Charlon T. (2019) <doi:10.13097/archive-ouverte/unige:161795>.

Thomas Charlon

opticskxi

OPTICS K-Xi Density-Based Clustering

dist_matrix function

<dl><dt>data</dt>
<dd>Rectangular numeric matrix [Observations, Features]</dd>
<dt>method</dt>
<dd>Methods accepted by amap::Dist or cosine and norm_inprod</dd>
<dt>n_cores</dt>
<dd>Number of cores</dd></dl>

Arguments

dist_matrix — dist_matrix

<dl>

<dt>data</dt>
<dd>Rectangular numeric matrix [Observations, Features]</dd>


<dt>method</dt>
<dd>Methods accepted by amap::Dist or cosine and norm_inprod</dd>


<dt>n_cores</dt>
<dd>Number of cores</dd>

</dl>

dist_matrix: dist_matrix

Description

Usage

Value

Arguments