GenAnno

Returns a vector of length = the number of columns (SNPs) in the genotype
matrix. Each SNP is classified as a benign missense variant (0), a
deleterious missense variant (1), or a protein truncating variant (2).

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. (2022) "An allelic series rare variant association test for candidate gene discovery" <doi:10.1101/2022.12.23.521658>.

Zachary McCaw

AllelicSeries

Allelic Series Test

Christoph Klein

insitro 

GenAnno function

<dl><dt>snps</dt>
<dd>Number of SNPs in the gene.</dd>
<dt>p_dmv</dt>
<dd>Frequency of deleterious missense variants.</dd>
<dt>p_ptv</dt>
<dd>Frequency of protein truncating variants.</dd></dl>

Arguments

Generate Genotype Annotations — GenAnno

<dl>

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


<dt>p_dmv</dt>
<dd>Frequency of deleterious missense variants.</dd>


<dt>p_ptv</dt>
<dd>Frequency of protein truncating variants.</dd>

</dl>

GenAnno: Generate Genotype Annotations

Description

Usage

Value

Arguments