RANDOM

Internal core function used in SEL.HAP() to fit mixed models and
test the random effect of a haplotype design matrix <code>z</code>.

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

RANDOM function

<dl><dt>z</dt>
<dd>Haplotype design matrix (n x r). When <code>PAR</code> is NULL,
<code>z</code> can be NULL and the function only estimates variance
components in the mixed model.</dd>
<dt>YFIX</dt>
<dd>A data.frame or matrix with phenotype in the first column
and fixed-effect covariates in the remaining columns.</dd>
<dt>KIN</dt>
<dd>A list of kinship matrices.</dd>
<dt>PAR</dt>
<dd>Optional vector of (log) variance components. If NULL, they
are estimated by the internal mixed model.</dd></dl>

Arguments

RANDOM: Mixed model and haplotype random effect test — RANDOM

<dl>

<dt>z</dt>
<dd>Haplotype design matrix (n x r). When <code>PAR</code> is NULL,
<code>z</code> can be NULL and the function only estimates variance
components in the mixed model.</dd>


<dt>YFIX</dt>
<dd>A data.frame or matrix with phenotype in the first column
and fixed-effect covariates in the remaining columns.</dd>


<dt>KIN</dt>
<dd>A list of kinship matrices.</dd>


<dt>PAR</dt>
<dd>Optional vector of (log) variance components. If NULL, they
are estimated by the internal mixed model.</dd>

</dl>

RANDOM: RANDOM: Mixed model and haplotype random effect test

Description

Usage

Value

Arguments