GenGeno

Generates genotypes in linkage equilibrium with accompanying annotations.

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 

GenGeno 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>
<dt>prop_anno</dt>
<dd>Proportions of annotations in each category. Length should
equal the number of annotation categories. Default of c(0.5, 0.4, 0.1) is
based on the approximate empirical frequencies of BMVs, DMVs, and PTVs.</dd></dl>

Arguments

Generate Genotypes — GenGeno

<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>


<dt>prop_anno</dt>
<dd>Proportions of annotations in each category. Length should
equal the number of annotation categories. Default of c(0.5, 0.4, 0.1) is
based on the approximate empirical frequencies of BMVs, DMVs, and PTVs.</dd>

</dl>

GenGeno: Generate Genotypes

Description

Usage

Value

Arguments