Abstract
MOTIVATION: In consensus clustering, a clustering algorithm is used in combination with a subsampling procedure to detect stable clusters. Previous studies on both simulated and real data suggest that consensus clustering outperforms native algorithms. RESULTS: We extend here consensus clustering to allow for attribute weighting in the calculation of pairwise distances using existing regularized approaches. We propose a procedure for the calibration of the number of clusters (and regularization parameter) by maximizing the sharp score, a novel stability score calculated directly from consensus clustering outputs, making it extremely computationally competitive. Our simulation study shows better clustering performances of (i) approaches calibrated by maximizing the sharp score compared to existing calibration scores and (ii) weighted compared to unweighted approaches in the presence of features that do not contribute to cluster definition. Application on real gene expression data measured in lung tissue reveals clear clusters corresponding to different lung cancer subtypes. AVAILABILITY AND IMPLEMENTATION: The R package sharp (version ≥1.4.3) is available on CRAN at https://CRAN.R-project.org/package=sharp.