GenGenoMat

Generate genotypes for <code>n</code> subject at <code>snps</code> variants in linkage
equilibrium. Genotypes are generated such that the MAC is always &gt;= 1.

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 

GenGenoMat function

<dl><dt>n</dt>
<dd>Sample size.</dd>
<dt>snps</dt>
<dd>Number of SNP in the gene.</dd>
<dt>maf_range</dt>
<dd>Range of minor allele frequencies: c(MIN, MAX).</dd></dl>

Arguments

Generate Genotype Matrix — GenGenoMat

<dl>

<dt>n</dt>
<dd>Sample size.</dd>


<dt>snps</dt>
<dd>Number of SNP in the gene.</dd>


<dt>maf_range</dt>
<dd>Range of minor allele frequencies: c(MIN, MAX).</dd>

</dl>

GenGenoMat: Generate Genotype Matrix

Description

Usage

Value

Arguments