fitNullModel.POLMM

Initializes the POLMM null model from an ordered categorical response and
covariate matrix, preparing C++ state for subsequent marker/region tests.

internal

Provides a comprehensive suite of genome-wide association study (GWAS) methods
specifically designed for biobank-scale data, including but not limited to, robust approaches
for time-to-event traits (Li et al., 2025 <doi:10.1038/s43588-025-00864-z>) and ordinal
categorical traits (Bi et al., 2021 <doi:10.1016/j.ajhg.2021.03.019>). The package also offers
general frameworks for GWAS of any trait type (Bi et al., 2020 <doi:10.1016/j.ajhg.2020.06.003>),
while accounting for sample relatedness (Xu et al., 2025 <doi:10.1038/s41467-025-56669-1>) or
population structure (Ma et al., 2025 <doi:10.1186/s13059-025-03827-9>). By accurately
approximating score statistic distributions using saddlepoint approximation (SPA), these
methods can effectively control type I error rates for rare variants and in the presence of
unbalanced phenotype distributions. Additionally, the package 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

fitNullModel.POLMM function

<dl><dt>response</dt>
<dd>Ordered factor response (lowest level coded as 0 internally).</dd>
<dt>designMat</dt>
<dd>Numeric covariate matrix or data.frame (n x p).</dd>
<dt>subjData</dt>
<dd>Character vector of subject IDs aligned with rows of
<code>designMat</code> and <code>response</code>.</dd>
<dt>control</dt>
<dd>List of POLMM options (e.g., <code>tau</code>,
<code>maxMissingVarRatio</code>, <code>minMafVarRatio</code>).</dd>
<dt>optionGRM</dt>
<dd>Character, either <code>"DenseGRM"</code> or <code>"SparseGRM"</code>.</dd>
<dt>GenoFile</dt>
<dd>Character, path to genotype file (PLINK or BGEN format).</dd>
<dt>GenoFileIndex</dt>
<dd>Character or NULL, path to genotype index files.
If NULL, uses same prefix as <code>GenoFile</code>.</dd>
<dt>SparseGRMFile</dt>
<dd>Character or NULL, path to sparse GRM file.
If provided, sparse GRM is used; otherwise dense GRM is constructed.</dd></dl>

Arguments

Fit POLMM null model for ordinal outcomes — fitNullModel.POLMM

<dl>

<dt>response</dt>
<dd>Ordered factor response (lowest level coded as 0 internally).</dd>


<dt>designMat</dt>
<dd>Numeric covariate matrix or data.frame (n x p).</dd>


<dt>subjData</dt>
<dd>Character vector of subject IDs aligned with rows of
<code>designMat</code> and <code>response</code>.</dd>


<dt>control</dt>
<dd>List of POLMM options (e.g., <code>tau</code>,
<code>maxMissingVarRatio</code>, <code>minMafVarRatio</code>).</dd>


<dt>optionGRM</dt>
<dd>Character, either <code>"DenseGRM"</code> or <code>"SparseGRM"</code>.</dd>


<dt>GenoFile</dt>
<dd>Character, path to genotype file (PLINK or BGEN format).</dd>


<dt>GenoFileIndex</dt>
<dd>Character or NULL, path to genotype index files.
If NULL, uses same prefix as <code>GenoFile</code>.</dd>


<dt>SparseGRMFile</dt>
<dd>Character or NULL, path to sparse GRM file.
If provided, sparse GRM is used; otherwise dense GRM is constructed.</dd>

</dl>

fitNullModel.POLMM: Fit POLMM null model for ordinal outcomes

Description

Usage

Value

Arguments