CHAP-GWAS: Leveraging Chromosomal Haplotypes to Improve Genome-Wide Association Studies R package CHAPGWAS version 0.1.3 CHAP-GWAS (Chromosomal Haplotype-Integrated Genome-Wide Association Study) provides a dynamically adaptive framework for genome-wide association studies (GWAS) that integrates chromosome-scale haplotypes with single nucleotide polymorphism (SNP) analysis. The method identifies and extends haplotype variants based on their phenotypic associations rather than predefined linkage blocks, enabling high-resolution detection of quantitative trait loci (QTL). By leveraging long-range phased haplotype information, CHAP-GWAS improves statistical power and offers a more comprehensive view of the genetic architecture underlying complex traits. Software Depends: R (>= 4.0.0) Imports: MASS, plyr Shibo Wang <shibow@ucr.edu> Comprehensive R Archive Network (CRAN) Shibo Wang [aut, cre], Qiong Jia [aut], Zhenyu Jia [aut, ctb] GPL-3 2026-01-08 application/tgz https://CRAN.R-project.org/package=CHAPGWAS doi:10.32614/CRAN.package.CHAPGWAS