BaselineSS

Baseline Counts Test from Sumstats

Implementation of gene-level rare variant association tests targeting allelic series: genes where increasingly deleterious mutations have increasingly large phenotypic effects. The COding-variant Allelic Series Test (COAST) operates on the benign missense variants (BMVs), deleterious missense variants (DMVs), and protein truncating variants (PTVs) within a gene. COAST uses a set of adjustable weights that tailor the test towards rejecting the null hypothesis for genes where the average magnitude of effect increases monotonically from BMVs to DMVs to PTVs. See McCaw ZR, O’Dushlaine C, Somineni H, Bereket M, Klein C, Karaletsos T, Casale FP, Koller D, Soare TW. (2023) "An allelic series rare variant association test for candidate gene discovery" <doi:10.1016/j.ajhg.2023.07.001>.

Zachary McCaw

AllelicSeries

Allelic Series Test

Christoph Klein

Thomas Soare

Jianhui Gao

insitro 

BaselineSS function

<dl><dt>anno</dt>
<dd>(snps x 1) annotation vector with integer values in 1 through
the number of annotation categories L.</dd>
<dt>beta</dt>
<dd>(snps x 1) vector of effect sizes for
the coding genetic variants within a gene.</dd>
<dt>ld</dt>
<dd>(snps x snps) matrix of correlations among the genetic variants.</dd>
<dt>se</dt>
<dd>(snps x 1) vector of standard errors for the effect sizes.</dd>
<dt>n_anno</dt>
<dd>Number of annotation categories L.</dd>
<dt>return_beta</dt>
<dd>Return estimated effect sizes and standard errors?
Default: FALSE.</dd></dl>

Arguments

Baseline Counts Test from Sumstats — BaselineSS

<dl>

<dt>anno</dt>
<dd>(snps x 1) annotation vector with integer values in 1 through
the number of annotation categories L.</dd>


<dt>beta</dt>
<dd>(snps x 1) vector of effect sizes for
the coding genetic variants within a gene.</dd>


<dt>ld</dt>
<dd>(snps x snps) matrix of correlations among the genetic variants.</dd>


<dt>se</dt>
<dd>(snps x 1) vector of standard errors for the effect sizes.</dd>


<dt>n_anno</dt>
<dd>Number of annotation categories L.</dd>


<dt>return_beta</dt>
<dd>Return estimated effect sizes and standard errors?
Default: FALSE.</dd>

</dl>

BaselineSS: Baseline Counts Test from Sumstats

Description

Usage

Value

Arguments