Estimates the gene-environment correlation (rGE) and tests for a GxE using a residual environmental score. If there is an important correlation between G and E, the model is still valid prediction-wise but the interpretation is affected as the question becomes: is it really a GxE or a GxG since E is partially caused by G? To account for this, we remove the influence of G on E (If E = b0 + b1*G + e, we use E_resid = E - b1*G) and refit the model to see if the model parameters changed. The residual environmental score (E_resid) is uncorrelated with G. This does not account for passive rGE but only active rGE.

Constructs genotype x environment interaction (GxE) models where
G is a weighted sum of genetic variants (genetic score) and E is a weighted
sum of environments (environmental score) using the alternating optimization algorithm
by Jolicoeur-Martineau et al. (2017) <arXiv:1703.08111>. This approach has greatly
enhanced predictive power over traditional GxE models which include only a single
genetic variant and a single environmental exposure. Although this approach was
originally made for GxE modelling, it is flexible and does not require the use of
genetic and environmental variables. It can also handle more than 2 latent variables
(rather than just G and E) and 3-way interactions or more. The LEGIT model produces
highly interpretable results and is very parameter-efficient thus it can even be
used with small sample sizes (n < 250). Tools to determine the type of interaction
(vantage sensitivity, diathesis-stress or differential susceptibility), with any
number of genetic variants or environments, are available <arXiv:1712.04058>. The
software can now produce mixed-effects LEGIT models through the lme4 package.

Alexia Jolicoeur-Martineau

LEGIT

Latent Environmental & Genetic InTeraction (LEGIT) Model

rGE function

<dl><dt>object</dt>
<dd>An object of class "LEGIT" or "IMLEGIT".</dd>
<dt>...</dt>
<dd>Further arguments passed to or from other methods.</dd></dl>

Arguments

Gene-Environment correlation estimation and testing — rGE

<dl>

<dt>object</dt>
<dd>An object of class "LEGIT" or "IMLEGIT".</dd>


<dt>...</dt>
<dd>Further arguments passed to or from other methods.</dd>

</dl>

rGE: Gene-Environment correlation estimation and testing

Description

Usage

Arguments