RegionScan: A comprehensive R package for region-level genome-wide association testing with integration and visualization of multiple-variant and single-variant hypothesis testing

Abstract

SummaryRegionScan is an R package for comprehensive and scalable genome-wide association testing of region-level multiple-variant and single-variant statistics and visualization of the results. It implements various state-of-the-art region-level tests to improve signal detection under heterogeneous genetic architectures and facilitates comparison of multiple-variant region-level and single-variant test results. It exploits local linkage disequilibrium (LD) structure for genomic partitioning and LD-adaptive region definition. RegionScan is compatible with VCF input file formats for genotyped and imputed variants, and options are available for analysis of multi-allelic variants and unbalanced binary phenotypes. It accommodates parallel region-level processing and analysis to improve computational time and memory efficiency and provides detailed outputs and utility functions to assist results comparison, visualization, and interpretation. Availability and implementationRegionScan is freely available for download on GitHub (https://github.com/brossardMyriam/RegionScan). Contactbull@lunenfeld.ca, brossard@lunenfeld.ca. Supplementary informationSupplementary data are available at Bioinformatics online.