prepare_plot_data

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

prepare_plot_data function

<dl><dt>multi.dat</dt>
<dd>multi trait cophescan results returned from cophe.multitrait or multitrait.simplify</dd>
<dt>querysnpid</dt>
<dd>query variant</dd>
<dt>query_trait_names</dt>
<dd>vector of names of the query traits</dd>
<dt>thresh_Ha</dt>
<dd>Ha threshold to be displayed</dd>
<dt>thresh_Hc</dt>
<dd>Hc threshold to be displayed</dd>
<dt>hmp</dt>
<dd>return for heatmap</dd>
<dt>cophe.plot</dt>
<dd>default: TRUE, return for <code>cophe_plot</code></dd></dl>

Arguments

Prepare data for plotting — prepare_plot_data

<dl>

<dt>multi.dat</dt>
<dd>multi trait cophescan results returned from cophe.multitrait or multitrait.simplify</dd>


<dt>querysnpid</dt>
<dd>query variant</dd>


<dt>query_trait_names</dt>
<dd>vector of names of the query traits</dd>


<dt>thresh_Ha</dt>
<dd>Ha threshold to be displayed</dd>


<dt>thresh_Hc</dt>
<dd>Hc threshold to be displayed</dd>


<dt>hmp</dt>
<dd>return for heatmap</dd>


<dt>cophe.plot</dt>
<dd>default: TRUE, return for <code>cophe_plot</code></dd>

</dl>

prepare_plot_data: Prepare data for plotting

Description

Usage

Value

Arguments

See Also