fitNullModel.SPACox

Computes martingale residuals (or uses provided residuals) and an empirical
cumulant generating function (CGF) for SPA-based single-variant 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.SPACox function

<dl><dt>response</dt>
<dd>Either a <code><a href="/link/survival%3A%3ASurv?package=GRAB&version=0.2.4" data-mini-rdoc="GRAB::survival::Surv">survival::Surv</a></code> object (time-to-event) or a
numeric residual vector with class <code>"Residual"</code>.</dd>
<dt>designMat</dt>
<dd>Numeric design matrix (n x p) of covariates.</dd>
<dt>subjData</dt>
<dd>Vector of subject IDs aligned with rows of <code>designMat</code>.</dd>
<dt>control</dt>
<dd>List with fields such as <code>range</code> and <code>length.out</code>
for the CGF grid.</dd>
<dt>...</dt>
<dd>Extra arguments passed to <code><a href="/link/survival%3A%3Acoxph?package=GRAB&version=0.2.4" data-mini-rdoc="GRAB::survival::coxph">survival::coxph</a></code> when
<code>response</code> is <code>Surv</code>.</dd></dl>

Arguments

Fit SPACox null model from survival outcomes or residuals — fitNullModel.SPACox

<dl>

<dt>response</dt>
<dd>Either a <code><a href='https://rdrr.io/pkg/survival/man/Surv.html'>survival::Surv</a></code> object (time-to-event) or a
numeric residual vector with class <code>"Residual"</code>.</dd>


<dt>designMat</dt>
<dd>Numeric design matrix (n x p) of covariates.</dd>


<dt>subjData</dt>
<dd>Vector of subject IDs aligned with rows of <code>designMat</code>.</dd>


<dt>control</dt>
<dd>List with fields such as <code>range</code> and <code>length.out</code>
for the CGF grid.</dd>


<dt>...</dt>
<dd>Extra arguments passed to <code><a href='https://rdrr.io/pkg/survival/man/coxph.html'>survival::coxph</a></code> when
<code>response</code> is <code>Surv</code>.</dd>

</dl>

fitNullModel.SPACox: Fit SPACox null model from survival outcomes or residuals

Description

Usage

Value

Arguments