CheckInputsSS

Input Checks for Summary Statistics

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 

CheckInputsSS function

<dl><dt>anno</dt>
<dd>(snps x 1) annotation vector with values in c(0, 1, 2).</dd>
<dt>beta</dt>
<dd>(snps x 1) vector of effect sizes for the coding genetic variants
within a gene.</dd>
<dt>se</dt>
<dd>(snps x 1) vector of standard errors for the effect sizes.</dd>
<dt>lambda</dt>
<dd>Genomic inflation factor.</dd>
<dt>ld</dt>
<dd>(snps x snps) matrix of correlations among the genetic variants.
Although ideally provided, an identity matrix is assumed if not.</dd>
<dt>weights</dt>
<dd>(L x 1) annotation category weights.</dd>
<dt>is_skat</dt>
<dd>Logical, is the check for the SKAT test?</dd>
<dt>maf</dt>
<dd>(snps x 1) vector of minor allele frequencies. Although ideally
provided, defaults to the zero vector.</dd></dl>

Arguments

Input Checks for Summary Statistics — CheckInputsSS

<dl>

<dt>anno</dt>
<dd>(snps x 1) annotation vector with values in c(0, 1, 2).</dd>


<dt>beta</dt>
<dd>(snps x 1) vector of effect sizes for the coding genetic variants
within a gene.</dd>


<dt>se</dt>
<dd>(snps x 1) vector of standard errors for the effect sizes.</dd>


<dt>lambda</dt>
<dd>Genomic inflation factor.</dd>


<dt>ld</dt>
<dd>(snps x snps) matrix of correlations among the genetic variants.
Although ideally provided, an identity matrix is assumed if not.</dd>


<dt>weights</dt>
<dd>(L x 1) annotation category weights.</dd>


<dt>is_skat</dt>
<dd>Logical, is the check for the SKAT test?</dd>


<dt>maf</dt>
<dd>(snps x 1) vector of minor allele frequencies. Although ideally
provided, defaults to the zero vector.</dd>

</dl>

CheckInputsSS: Input Checks for Summary Statistics

Description

Usage

Value

Arguments