PA_algorithm

Title Pearson-Aitken algorithm to calculate mean values in truncated multivariate normal distributions

Implementation of several phenotype-based family genetic risk scores
with unified input data and data preparation functions to help facilitate
the required data preparation and management. The implemented family genetic
risk scores are the extended liability threshold model conditional on family history (LT-FH++)
from Pedersen (2022) <doi:10.1016/j.ajhg.2022.01.009> and Pedersen (2023) <https://www.nature.com/articles/s41467-023-41210-z>,
Pearson-Aitken Family Genetic Risk Scores (PA-FGRS) from Krebs (2024) <doi:10.1016/j.ajhg.2024.09.009>,
and family genetic risk score by Kendler (2021) <doi:10.1001/jamapsychiatry.2021.0336>.

Emil Michael Pedersen

LTFGRS

Implementation of Several Phenotype-Based Family Genetic Risk
Scores

Jette Steinbach

Lucas Rasmussen

Morten Dybdahl Krebs

PA_algorithm function

<dl><dt>mu</dt>
<dd>vector of means</dd>
<dt>covmat</dt>
<dd>covariance matrix, contaning kinship coefficient and heritability on each entry (except diagnoal, which is 1 for full liabilities and h2 for genetic liabilities)</dd>
<dt>target_id</dt>
<dd>ID of target individual (or genetic liability), i.e. rowname in covmat to return expected genetic liability for</dd>
<dt>lower</dt>
<dd>vector of lower thresholds</dd>
<dt>upper</dt>
<dd>vector of upper thresholds</dd>
<dt>K_i</dt>
<dd>vector of stratified CIPs for each individual. Only used for estimating genetic liability under the mixture model.</dd>
<dt>K_pop</dt>
<dd>vector of population CIPs. Only used for estimating genetic liability under the mixture model.</dd></dl>

Arguments

Title Pearson-Aitken algorithm to calculate mean values in truncated multivariate normal distributions — PA_algorithm

<dl>

<dt>mu</dt>
<dd>vector of means</dd>


<dt>covmat</dt>
<dd>covariance matrix, contaning kinship coefficient and heritability on each entry (except diagnoal, which is 1 for full liabilities and h2 for genetic liabilities)</dd>


<dt>target_id</dt>
<dd>ID of target individual (or genetic liability), i.e. rowname in covmat to return expected genetic liability for</dd>


<dt>lower</dt>
<dd>vector of lower thresholds</dd>


<dt>upper</dt>
<dd>vector of upper thresholds</dd>


<dt>K_i</dt>
<dd>vector of stratified CIPs for each individual. Only used for estimating genetic liability under the mixture model.</dd>


<dt>K_pop</dt>
<dd>vector of population CIPs. Only used for estimating genetic liability under the mixture model.</dd>

</dl>

PA_algorithm: Title Pearson-Aitken algorithm to calculate mean values in truncated multivariate normal distributions

Description

Usage

Value

Arguments