wakefield_pp

This function was adapted from its namesake in cupcake package (github.com/ollyburren/cupcake/) to no longer require allele frequencies.

Quickly computes polygenic scores from GWAS summary statistics of either case-control or quantitative traits without parameter tuning. Reales,G., Vigorito, E., Kelemen,M., Wallace,C. (2021) <doi:10.1101/2020.07.24.220392> "RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset".

Guillermo Reales

RapidoPGS

A Fast and Light Package to Compute Polygenic Risk Scores

Chris Wallace

Olly Burren

wakefield_pp function

<dl><dt>beta</dt>
<dd>a vector of effect sizes (\(\beta\)) from a quantitative trait GWAS</dd>
<dt>se</dt>
<dd>vector of standard errors of effect sizes (\(\beta\))</dd>
<dt>pi_i</dt>
<dd>a scalar representing the prior probability (DEFAULT \(1 \times 10^{-4}\))</dd>
<dt>sd.prior</dt>
<dd>a scalar representing our prior expectation of \(\beta\) (DEFAULT 0.2).
The method assumes a normal prior on the population log relative risk centred at 0 and the DEFAULT
value sets the variance of this distribution to 0.04, equivalent to a 95\
is in the range of 0.66-1.5 at any causal variant.</dd></dl>

Arguments

Olly Burren, Chris Wallace, Guillermo Reales

Author

compute posterior probabilities using Wakefield's approximate Bayes Factors
wakefield_pp computes posterior probabilities for a given SNP to be causal for a given SNP under the assumption of a single causal variant. — wakefield_pp

<dl>

<dt>beta</dt>
<dd>a vector of effect sizes (\(\beta\)) from a quantitative trait GWAS</dd>


<dt>se</dt>
<dd>vector of standard errors of effect sizes (\(\beta\))</dd>


<dt>pi_i</dt>
<dd>a scalar representing the prior probability (DEFAULT \(1 \times 10^{-4}\))</dd>


<dt>sd.prior</dt>
<dd>a scalar representing our prior expectation of \(\beta\) (DEFAULT 0.2).
The method assumes a normal prior on the population log relative risk centred at 0 and the DEFAULT
value sets the variance of this distribution to 0.04, equivalent to a 95\
is in the range of 0.66-1.5 at any causal variant.</dd>

</dl>

compute posterior probabilities using Wakefield's approximate Bayes Factors
<code>wakefield_pp</code> computes posterior probabilities for a given SNP to be causal for a given SNP under the assumption of a single causal variant.

wakefield_pp: compute posterior probabilities using Wakefield's approximate Bayes Factors `wakefield_pp` computes posterior probabilities for a given SNP to be causal for a given SNP under the assumption of a single causal variant.

Description

Usage

Value

Arguments

Author