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n <- 1e3 | |
t <- 1e3 | |
covar_effect <- 1 | |
trt_effect <- 0 #0.1 | |
null_no_covar <- alt_no_covar <- null_yes_covar <- alt_yes_covar <- rep(NA, t) | |
for (i in 1:t) { | |
covar <- rnorm(n = n) | |
snp <- rnorm(n = n) | |
y <- rnorm(n = n, mean = covar*covar_effect + snp*trt_effect) | |
null_no_covar[i] <- logLik(object = lm(formula = y ~ 1)) | |
alt_no_covar[i] <- logLik(lm(formula = y ~ snp)) | |
null_yes_covar[i] <- logLik(lm(formula = y ~ covar)) | |
alt_yes_covar[i] <- logLik(lm(formula = y ~ covar + snp)) | |
} | |
my_line <- function(x, y, ...){ | |
points(x, y, ...) | |
abline(a = 0, b = 1,...) | |
} | |
no_covar_LRS <- 2*(alt_no_covar - null_no_covar) | |
yes_covar_LRS <- 2*(alt_yes_covar - null_yes_covar) | |
pairs(x = data.frame(no_covar_LRS = sort(pchisq(q = no_covar_LRS, df = 1)), | |
yes_covar_LRS = sort(pchisq(q = yes_covar_LRS, df = 1)), | |
unif = seq(from = 0.5/t, to = 1 - 0.5/t, length.out = t)), | |
panel = my_line, | |
upper.panel = NULL) |
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