Aggregator

Aggregates genotypes within annotation categories.

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 

Aggregator 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>drop_empty</dt>
<dd>Drop empty columns? Default: TRUE.</dd>
<dt>indicator</dt>
<dd>Convert raw counts to indicators? Default: FALSE.</dd>
<dt>method</dt>
<dd>Method for aggregating across categories:
("none", "max", "sum"). Default: "none".</dd>
<dt>min_mac</dt>
<dd>Minimum minor allele count for inclusion. Default: 0.</dd>
<dt>weights</dt>
<dd>(L x 1) vector of annotation category weights. Note that the
number of annotation categories L is inferred from the length of <code>weights</code>.</dd></dl>

Arguments

<ul>
<li>Ensure the length of the <code>weights</code> vector matches the total number of
annotation categories.</li>
<li>The <code>weights</code> essentially scales the minor allele count in the <code>l</code>th
category by <code>weights[l]</code>.</li>
</ul>

Notes

Aggregator — Aggregator

<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>drop_empty</dt>
<dd>Drop empty columns? Default: TRUE.</dd>


<dt>indicator</dt>
<dd>Convert raw counts to indicators? Default: FALSE.</dd>


<dt>method</dt>
<dd>Method for aggregating across categories:
("none", "max", "sum"). Default: "none".</dd>


<dt>min_mac</dt>
<dd>Minimum minor allele count for inclusion. Default: 0.</dd>


<dt>weights</dt>
<dd>(L x 1) vector of annotation category weights. Note that the
number of annotation categories L is inferred from the length of <code>weights</code>.</dd>

</dl>

<ul>
<li>Ensure the length of the <code>weights</code> vector matches the total number of
annotation categories.</li>
<li>The <code>weights</code> essentially scales the minor allele count in the <code>l</code>th
category by <code>weights[l]</code>.</li>
</ul>

Aggregator: Aggregator

Description

Usage

Value

Arguments

Notes