CalcRegParam

Calculate phenotypic regression coefficients and the residual variation
based on proportion of variation explained (PVE) by each factor. Note that
the proportion of variation explained by genotype is required, but genetic
effects are not generated here.

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 

CalcRegParam function

<dl><dt>pve_age</dt>
<dd>PVE by age.</dd>
<dt>pve_pcs</dt>
<dd>PVE by PCs (collectively).</dd>
<dt>pve_sex</dt>
<dd>PVE by sex.</dd></dl>

Arguments

Calculate Regression Parameters — CalcRegParam

<dl>

<dt>pve_age</dt>
<dd>PVE by age.</dd>


<dt>pve_pcs</dt>
<dd>PVE by PCs (collectively).</dd>


<dt>pve_sex</dt>
<dd>PVE by sex.</dd>

</dl>

CalcRegParam: Calculate Regression Parameters

Description

Usage

Value

Arguments