cophe.bf_bf

a dataset represented by Bayes factors from SuSIE

internal

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.bf_bf function

<dl><dt>sus_dat</dt>
<dd>a list with the output of running susie</dd>
<dt>cred_set</dt>
<dd>credible set extracted from susie</dd>
<dt>querysnpid</dt>
<dd>Id of the query variant</dd>
<dt>querytrait</dt>
<dd>Query trait name</dd>
<dt>pn</dt>
<dd>prior probability that none of the SNPs/variants in the region are associated with the query trait</dd>
<dt>pa</dt>
<dd>prior probability that a non-query variant is causally associated with the query trait</dd>
<dt>pc</dt>
<dd>prior probability that the query variant is causally associated with the query trait</dd></dl>

Arguments

extract data through Bayes factors — cophe.bf_bf

<dl>

<dt>sus_dat</dt>
<dd>a list with the output of running susie</dd>


<dt>cred_set</dt>
<dd>credible set extracted from susie</dd>


<dt>querysnpid</dt>
<dd>Id of the query variant</dd>


<dt>querytrait</dt>
<dd>Query trait name</dd>


<dt>pn</dt>
<dd>prior probability that none of the SNPs/variants in the region are associated with the query trait</dd>


<dt>pa</dt>
<dd>prior probability that a non-query variant is causally associated with the query trait</dd>


<dt>pc</dt>
<dd>prior probability that the query variant is causally associated with the query trait</dd>

</dl>

cophe.bf_bf: extract data through Bayes factors

Description

Usage

Value

Arguments

See Also