RegionScan : A comprehensive R package for region-level genome-wide association testing with integration and visualization of multiple-variant and single-variant hypothesis testing
RegionScan is a R package for comprehensive and scalable region-level genome-wide association testing of alternative 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 comparison of multiple-variant region-level and single-variant test results. It leverages LD-based genomic partitioning for LD-adaptive region definition. RegionScan is compatible with VCF input file format, and accommodates parallel region-level processing and analysis to improve computational time and memory efficiency. It also provide options for analysis of multi-allelic variants, unbalanced binary phenotypes, with detailed outputs for results interpretation, and utility functions for visualization, comparison, and interpretation.
The detailed information about RegionScan can be found in our in our preprint.
Use the devtools package (available from
CRAN) to
install automatically from this repository:
library(devtools)
install_github("brossardMyriam/RegionScan")
See the tutorial for an illustration on how to use RegionScan on the realistic example dataset provided with the package.
Overview of RegionScan for genome-wide region-level association analysis on chr19 (to facilitate visualization) in a Usage case study (see details in our preprint).
- Myriam Brossard (brossard@lunenfeld.ca), author and main developer
- Yun J Yoo, contributor
RegionScan : A comprehensive R package for region-level genome-wide association testing with integration and visualization of multiple-variant and single-variant hypothesis testing. Brossard M, Roshandel D, Luo K, Yavartanoo F, Paterson AD, Yoo YJ, Bull SB. DOI: https://www.biorxiv.org/content/10.1101/2024.03.04.582374v1
This package is released under the GNU General Public License (GPL) v3.0.