Batcheffect.Test

This function test for the allele frequency difference between the study cohort and the external datasets.

Provides a comprehensive suite of genome-wide association study (GWAS) methods
specifically designed for biobank-scale data. The package offers computationally efficient
and robust association tests for time-to-event traits (e.g., Bi et al., 2020
<doi:10.1016/j.ajhg.2020.06.003>), ordinal categorical traits (e.g., Bi et al., 2021
<doi:10.1016/j.ajhg.2021.03.019>), and longitudinal traits (Xu et al., 2025
<doi:10.1038/s41467-025-56669-1>). Additionally, it includes functions for
simulating genotype and phenotype data to support research and method development.

Woody Miao

GRAB

Genome-Wide Robust Analysis for Biobank Data (GRAB)

Wenjian Bi

Wei Zhou

Rounak Dey

Zhangchen Zhao

Seunggeun Lee

Batcheffect.Test function

<dl><dt>n0</dt>
<dd>A numeric. The sample size of cases in the study cohort</dd>
<dt>n1</dt>
<dd>A numeric. The sample size of controls in the study cohort</dd>
<dt>n.ext</dt>
<dd>A numeric. The sample size of external datasets</dd>
<dt>maf0</dt>
<dd>A numeric. The MAF of the cases.</dd>
<dt>maf1</dt>
<dd>A numeric. The MAF of the controls</dd>
<dt>maf.ext</dt>
<dd>A numeric. The MAF of the external datasets.</dd>
<dt>pop.prev</dt>
<dd>A numeric. The population prevalence of the disease.</dd>
<dt>var.ratio</dt>
<dd>A numeric. The variance ratio calculated by sparseGRM.</dd></dl>

Arguments

Test for batch effect — Batcheffect.Test

<dl>

<dt>n0</dt>
<dd>A numeric. The sample size of cases in the study cohort</dd>


<dt>n1</dt>
<dd>A numeric. The sample size of controls in the study cohort</dd>


<dt>n.ext</dt>
<dd>A numeric. The sample size of external datasets</dd>


<dt>maf0</dt>
<dd>A numeric. The MAF of the cases.</dd>


<dt>maf1</dt>
<dd>A numeric. The MAF of the controls</dd>


<dt>maf.ext</dt>
<dd>A numeric. The MAF of the external datasets.</dd>


<dt>pop.prev</dt>
<dd>A numeric. The population prevalence of the disease.</dd>


<dt>var.ratio</dt>
<dd>A numeric. The variance ratio calculated by sparseGRM.</dd>

</dl>

Batcheffect.Test: Test for batch effect

Description

Usage

Value

Arguments