penetrances <- list("strong_dominant" = c(0.05, 0.05, 0.05,
0.05, 0.80, 0.80,
0.05, 0.80, 0.80),
"weak_dominant" = c(0.05, 0.05, 0.05,
0.05, 0.50, 0.50,
0.05, 0.50, 0.50),
"strong_additive" = c(0.05, 0.05, 0.05,
0.05, 0.40, 0.50,
0.05, 0.50, 0.80),
"weak_additive" = c(0.05, 0.05, 0.05,
0.05, 0.25, 0.30,
0.05, 0.30, 0.50),
"no_marginal" = c(0.492, 0.664, 0.481, # Velez Model No. 15
0.642, 0.330, 0.746,
0.656, 0.396, 0))
Xnew <- generate_samples_new_simulation(data = penetrances,
job = "1234",
first_pop = "strong_dominant",
second_pop = "strong_dominant",
sample_size = 500,
maf = .2,
n.snp = 20)
Ynew <- replicate(n = nrow(Xnew), expr = c())
for (i in 1:nrow(Xnew)){
if (Xnew$first_pop_status[i]){
Ynew[[i]] <- c(Ynew[[i]], 1)
}
if (Xnew$second_pop_status[i]){
Ynew[[i]] <- c(Ynew[[i]], 2)
}
}
Xnew <- Xnew[, 1:20]
Xold <- generate_samples_old_simulation(sample_size = 3000,
data = penetrances,
first_pop = "strong_dominant",
second_pop = "strong_dominant")
Yold <- Xold$classification
Xold <- Xold$designmatrix[]
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