loglik

A Bayesian method for Phenome-wide association studies (PheWAS) that identifies causal associations between genetic variants and traits, while simultaneously addressing confounding due to linkage disequilibrium. For details see
Manipur et al (2024, Nature Communications) <doi:10.1038/s41467-024-49990-8>.

Ichcha Manipur

cophescan

Adaptation of the Coloc Method for PheWAS

Chris Wallace

loglik function

<dl><dt>params</dt>
<dd>Vector of parameters: \(\alpha\), \(\beta\) and \(\gamma\)</dd>
<dt>lbf_mat</dt>
<dd>matrix of log bayes factors: lBF.Ha and lBF.Hc</dd>
<dt>nsnps</dt>
<dd>number of snps</dd>
<dt>covar_vec</dt>
<dd>Vector of the covariate</dd>
<dt>covar</dt>
<dd>logical: should the covariate inflormation be used? default: False</dd></dl>

Arguments

Log likelihood calculation — loglik

<dl>

<dt>params</dt>
<dd>Vector of parameters: \(\alpha\), \(\beta\) and \(\gamma\)</dd>


<dt>lbf_mat</dt>
<dd>matrix of log bayes factors: lBF.Ha and lBF.Hc</dd>


<dt>nsnps</dt>
<dd>number of snps</dd>


<dt>covar_vec</dt>
<dd>Vector of the covariate</dd>


<dt>covar</dt>
<dd>logical: should the covariate inflormation be used? default: False</dd>

</dl>

loglik: Log likelihood calculation

Description

Usage

Value

Arguments