test.HAP

test.HAP: Test haplotype effects for a local region

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.

Shibo Wang

CHAPGWAS

CHAP-GWAS: Leveraging Chromosomal Haplotypes to Improve
Genome-Wide Association Studies

Qiong Jia

Zhenyu Jia

test.HAP function

<dl><dt>HAP.X</dt>
<dd>Haplotype genotype matrix for a candidate genomic region.
Each column corresponds to a SNP within the region. Every two
consecutive rows correspond to the two homologous haplotypes of
the same individual (rows 1–2 = individual 1, rows 3–4 = individual 2, etc.).</dd>
<dt>YFIX</dt>
<dd>Phenotype and fixed-effect covariates.</dd>
<dt>KIN</dt>
<dd>List of kinship matrices.</dd>
<dt>PAR</dt>
<dd>Optional vector of variance components; if NULL, estimated internally.</dd></dl>

Arguments

test.HAP: Test haplotype effects for a local region — test.HAP

<dl>

<dt>HAP.X</dt>
<dd>Haplotype genotype matrix for a candidate genomic region.
Each column corresponds to a SNP within the region. Every two
consecutive rows correspond to the two homologous haplotypes of
the same individual (rows 1–2 = individual 1, rows 3–4 = individual 2, etc.).</dd>


<dt>YFIX</dt>
<dd>Phenotype and fixed-effect covariates.</dd>


<dt>KIN</dt>
<dd>List of kinship matrices.</dd>


<dt>PAR</dt>
<dd>Optional vector of variance components; if NULL, estimated internally.</dd>

</dl>

test.HAP: test.HAP: Test haplotype effects for a local region

Description

Usage

Value

Arguments