RegionScan

RegionScan implements region-level genome-wide association testing with integration and visualization of multiple-variant and single-variant statistics.

Key Features:

• Region-level tests: Implements various state-of-the-art region-level tests to improve signal detection under heterogeneous genetic architectures.
• LD-adaptive region definition: Exploits local linkage disequilibrium structure for genomic partitioning and LD-adaptive region definition.
• Input compatibility: Compatible with VCF input file formats for genotyped and imputed variants.
• Multi-allelic and unbalanced phenotype support: Provides options for analysis of multi-allelic variants and unbalanced binary phenotypes.
• Parallel processing: Accommodates parallel region-level processing and analysis to improve computational time and memory efficiency.
• Results comparison and visualization: Facilitates comparison of multiple-variant region-level and single-variant test results with detailed outputs and utility functions for visualization and interpretation.

Scientific Applications:

• Genome-wide association studies: Enables comprehensive and scalable genome-wide association testing at the region level.
• Genetic architecture analysis: Improves signal detection across diverse genetic architectures through integrated multiple-variant and single-variant testing approaches.
• Genomic partitioning: Supports LD-based genomic partitioning for adaptive region definition in association studies.

Methodology:

RegionScan exploits local linkage disequilibrium structure for genomic partitioning and LD-adaptive region definition, with parallel region-level processing and analysis.