line plot of permutations at 10, 100, and 1000

[smcclatchy]

showing spread of permutations

My permutation simulations.

thrs = rep(0, 100)
for(i in 1:100) {
tmp = scan1perm(genoprobs = pr, pheno = iron$pheno[,'liver', drop = F], Xcovar = Xcovar,
n_perm = 10)
thrs[i] = quantile(tmp, probs = 0.95)
}

thrs2 = rep(0, 100)
for(i in 1:100) {
tmp = scan1perm(genoprobs = pr, pheno = iron$pheno[,'liver', drop = F], Xcovar = Xcovar,
n_perm = 100)
thrs2[i] = quantile(tmp, probs = 0.95)
}

thrs3 = rep(0, 100)
for(i in 1:100) {
print(i)
tmp = scan1perm(genoprobs = pr, pheno = iron$pheno[,'liver', drop = F], Xcovar = Xcovar,
n_perm = 1000, cores = 4)
thrs3[i] = quantile(tmp, probs = 0.95)
}

data.frame(perm10 = thrs, perm100 = thrs2, perm1000 = thrs3) %>%
pivot_longer(cols = everything()) %>%
ggplot() +
geom_density(aes(value, color = name), size = 1) +
labs(title = 'Comparison of 0.05 threshold using 10 vs 100 permutation',
x = 'LOD', color = 'Num. Perms')