combine.abf

Internal function, calculate posterior probabilities for configurations, given logABFs for each SNP and prior probs

Performs the colocalisation tests described in
Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>,
Wallace (2020) <doi:10.1371/journal.pgen.1008720>,
Wallace (2021) <doi:10.1371/journal.pgen.1009440>.

Chris Wallace

coloc

Colocalisation Tests of Two Genetic Traits

Claudia Giambartolomei

Vincent Plagnol

combine.abf function

<dl><dt>l1</dt>
<dd>merged.df$lABF.df1</dd>
<dt>l2</dt>
<dd>merged.df$lABF.df2</dd>
<dt>p1</dt>
<dd>prior probability a SNP is associated with trait 1, default 1e-4</dd>
<dt>p2</dt>
<dd>prior probability a SNP is associated with trait 2, default 1e-4</dd>
<dt>p12</dt>
<dd>prior probability a SNP is associated with both traits, default 1e-5</dd>
<dt>quiet</dt>
<dd>don't print posterior summary if TRUE. default=FALSE</dd></dl>

Arguments

Claudia Giambartolomei, Chris Wallace

Author

combine.abf — combine.abf

<dl>

<dt>l1</dt>
<dd>merged.df$lABF.df1</dd>


<dt>l2</dt>
<dd>merged.df$lABF.df2</dd>


<dt>p1</dt>
<dd>prior probability a SNP is associated with trait 1, default 1e-4</dd>


<dt>p2</dt>
<dd>prior probability a SNP is associated with trait 2, default 1e-4</dd>


<dt>p12</dt>
<dd>prior probability a SNP is associated with both traits, default 1e-5</dd>


<dt>quiet</dt>
<dd>don't print posterior summary if TRUE. default=FALSE</dd>

</dl>

combine.abf: combine.abf

Description

Usage

Value

Arguments

Author