combine.bf

Calculate posterior probabilities for all the configurations

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

combine.bf function

<dl><dt>lBF_df</dt>
<dd>dataframe with log bayes factors of hypothesis Ha and Hn: column names should be lBF.Ha and lBF.Hc</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

Author

combine.bf — combine.bf

<dl>

<dt>lBF_df</dt>
<dd>dataframe with log bayes factors of hypothesis Ha and Hn: column names should be lBF.Ha and lBF.Hc</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>

combine.bf: combine.bf

Description

Usage

Value

Arguments

Author