crohn

The data set consist of 103 common (&gt;5% minor allele frequency) SNPs 
genotyped in 129 trios from an European-derived population. These 
SNPs are in a 500-kb region on human chromosome 5q31 implicated as 
containing a genetic risk factor for Crohn disease.
Imported from the gap R package.
An example use of the data is with the following paper,
Kelly M. Burkett, Celia M. T. Greenwood, BradMcNeney, Jinko Graham.
Gene genealogies for genetic association mapping, with application to Crohn's disease.
Fron Genet 2013, 4(260) doi: 10.3389/fgene.2013.00260

datasets

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>.

crohn: Crohn's disease data

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