example_2way_lme4: Simulated example of a 3 way interaction GxExZ model

In LEGIT: Latent Environmental & Genetic InTeraction (LEGIT) Model

Description

Simulated example of a 3 way interaction GxExZ model (where G, E and Z are latent variables).

g_j \sim Binomial(n=1,p=.30)

j = 1, 2, 3, 4

e_k \sim Normal(μ=0,σ=1.5)

k = 1, 2, 3

z_l \sim Normal(μ=3,σ=1)

l = 1, 2, 3

g = .2g_1 + .15g_2 - .3g_3 + .1g_4 + .05g_1g_3 + .2g_2g_3

e = -.45e_1 + .35e_2 + .2e_3

z = .15z_1 + .60z_2 + .25z_3

μ = -2 + 2g + 3e + z + 5ge - 1.5ez + 2gz + 2gez

y \sim Normal(μ=μ,σ=\code{sigma}) if logit=FALSE

y \sim Binomial(n=1,p=logit(μ)) if logit=TRUE

Usage

example_2way_lme4(N, sigma = 1, logit = FALSE, seed = NULL)

Arguments

N	Sample size.
sigma	Standard deviation of the gaussian noise (if logit=FALSE).
logit	If TRUE, the outcome is transformed to binary with a logit link.
seed	RNG seed.

Value

Returns a list containing, in the following order: data.frame with the observed outcome (with noise) and the true outcome (without noise), list containing the data.frame of the genetic variants (G), the data.frame of the e environments (E) and the data.frame of the z environments (Z), vector of the true genetic coefficients, vector of the true e environmental coefficients, vector of the true z environmental coefficients, vector of the true main model coefficients

Examples

# Doing only one iteration so its faster
train = example_2way_lme4(250, 1, seed=777)
D = train$data
G = train$G
E = train$E

F = y ~ G*E
fit = LEGIT(D, G, E, F, lme4=FALSE, maxiter=1)
summary(fit)
F = y ~ 1
fit_test = GxE_interaction_test(D, G, E, F, criterion="AIC", lme4=FALSE, maxiter=1)
fit_test
#fit_test = GxE_interaction_test(D, G, E, F, criterion="cv", lme4=FALSE, maxiter=1, cv_iter=1)
#fit_test

F = y ~ G*E + (1|subject)
fit = LEGIT(D, G, E, F, lme4=TRUE, maxiter=1)
summary(fit)
F = y ~ (1|subject)
fit_test = GxE_interaction_test(D, G, E, F, criterion="AIC", lme4=TRUE, maxiter=1)
fit_test
#fit_test = GxE_interaction_test(D, G, E, F, criterion="cv", lme4=TRUE, maxiter=1, cv_iter=1)
#fit_test

LEGIT documentation built on Jan. 12, 2022, 1:08 a.m.