CollapseGeno

Collapse variants with minor allele counts below the <code>min_mac</code> threshold
into an aggregated variant, separately within each variant category. Note
that the ordering of the variants will change, and that collapsing does not
guarantee that the resulting aggregate variant will itself have a
MAC greater than or equal to <code>min_mac</code>.

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 

CollapseGeno 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>geno</dt>
<dd>(n x snps) genotype matrix.</dd>
<dt>min_mac</dt>
<dd>Minimum minor allele count (MAC) for retention as an
individual variant. Variants with a MAC strictly less than the minimum
MAC will be collapsed into an aggregated variant, separately within
each annotation category.</dd></dl>

Arguments

Collapse Variants — CollapseGeno

<dl>

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


<dt>geno</dt>
<dd>(n x snps) genotype matrix.</dd>


<dt>min_mac</dt>
<dd>Minimum minor allele count (MAC) for retention as an
individual variant. Variants with a MAC strictly less than the minimum
MAC will be collapsed into an aggregated variant, separately within
each annotation category.</dd>

</dl>

CollapseGeno: Collapse Variants

Description

Usage

Value

Arguments