setDenseGRM

Set up a dense GRM (only for developers), other users can ignore this function

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

setDenseGRM function

<dl><dt>GenoFile</dt>
<dd>a character of genotype file. Three types of genotype files are supported: PLINK ("prefix.bed"), BGEN ("prefix.bgen"), and VCF ("prefix.vcf" or "prefix.vcf.gz").</dd>
<dt>GenoFileIndex</dt>
<dd>additional index files corresponding to the "GenoFile". If Null (default), the same prefix as GenoFile is used. PLINK: c("prefix.bim", "prefix.fam"), BGEN: c("prefix.bgi"), and VCF: c("prefix.vcf.tbi") or c("prefix.vcf.gz.tbi").</dd>
<dt>subjData</dt>
<dd>a character vector of subject IDs. Its order should be the same as the subjects order in the formula and data.</dd></dl>

Arguments

Set up a dense GRM (only for developers) — setDenseGRM

<dl>

<dt>GenoFile</dt>
<dd>a character of genotype file. Three types of genotype files are supported: PLINK ("prefix.bed"), BGEN ("prefix.bgen"), and VCF ("prefix.vcf" or "prefix.vcf.gz").</dd>


<dt>GenoFileIndex</dt>
<dd>additional index files corresponding to the "GenoFile". If Null (default), the same prefix as GenoFile is used. PLINK: c("prefix.bim", "prefix.fam"), BGEN: c("prefix.bgi"), and VCF: c("prefix.vcf.tbi") or c("prefix.vcf.gz.tbi").</dd>


<dt>subjData</dt>
<dd>a character vector of subject IDs. Its order should be the same as the subjects order in the formula and data.</dd>

</dl>

setDenseGRM: Set up a dense GRM (only for developers)

Description

Usage

Value

Arguments

Examples