plot_trait_manhat

Plot region Manhattan for a trait highlighting the queried variant

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

plot_trait_manhat function

<dl><dt>trait.dat</dt>
<dd>dataset used as input for running cophescan</dd>
<dt>querysnpid</dt>
<dd>the id of the causal variant as present in trait.dat$snp, plotted in red</dd>
<dt>alt.snpid</dt>
<dd>the id of the other variants as a vector to be plotted, plotted in blue</dd></dl>

Arguments

Plot region Manhattan for a trait highlighting the queried variant — plot_trait_manhat

<dl>

<dt>trait.dat</dt>
<dd>dataset used as input for running cophescan</dd>


<dt>querysnpid</dt>
<dd>the id of the causal variant as present in trait.dat$snp, plotted in red</dd>


<dt>alt.snpid</dt>
<dd>the id of the other variants as a vector to be plotted, plotted in blue</dd>

</dl>

plot_trait_manhat: Plot region Manhattan for a trait highlighting the queried variant

Description

Usage

Value

Arguments