cophe_heatmap

Heatmap of multi-trait cophescan results

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

cophe_heatmap function

<dl><dt>multi.dat</dt>
<dd>multi trait cophescan results returned from <code>cophe.multitrait</code> or formatted in the same way with multitrait.simplify</dd>
<dt>querysnpid</dt>
<dd>query variant</dd>
<dt>query_trait_names</dt>
<dd>names of phenotypes corresponding to the multi.dat results</dd>
<dt>thresh_Hc</dt>
<dd>Hc threshold to be displayed</dd>
<dt>thresh_Ha</dt>
<dd>Ha threshold to be displayed</dd>
<dt>...</dt>
<dd>additional arguments to be passed to
pheatmap</dd></dl>

Arguments

Heatmap of multi-trait cophescan results — cophe_heatmap

<dl>

<dt>multi.dat</dt>
<dd>multi trait cophescan results returned from <code>cophe.multitrait</code> or formatted in the same way with multitrait.simplify</dd>


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


<dt>query_trait_names</dt>
<dd>names of phenotypes corresponding to the multi.dat results</dd>


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


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


<dt>...</dt>
<dd>additional arguments to be passed to
pheatmap</dd>

</dl>

cophe_heatmap: Heatmap of multi-trait cophescan results

Description

Usage

Value

Arguments