CGHregions

CGHregions is a dimensionality-reduction method for array comparative genomic hybridization (array CGH) data that standardizes copy-number segment boundaries across samples to improve downstream analyses. It takes as input per-sample segmented log2-ratio profiles with discrete copy-number calls (e.g., from CGHcall) and “aligns” segmentation by adjusting breakpoints so that regions with similar breakpoint locations across multiple samples are represented with identical genomic boundaries. The resulting region-level representation reduces the number of features tested and improves comparability across cohorts, which can mitigate multiple-hypothesis-testing burden and support more robust downstream tasks such as association testing, clustering, and recurrent aberration detection.