Nothing
test_that("Overall check for binary phenotype.", {
# Note: binary phenotypes require a larger sample size.
withr::local_seed(101)
n <- 100
anno <- rep(c(1, 2, 3), each = 5)
geno <- replicate(15, stats::rbinom(n, size = 2, prob = 0.1))
eta <- -1 + geno %*% rep(c(0, 1, 2), each = 5)
null_pheno <- stats::rbinom(n, size = 1, prob = 0.5)
alt_pheno <- stats::rbinom(n, size = 1, prob = 1 / (1 + exp(-eta)))
# Note: the invisible(capture.output({})) wrapper is used because SKAT
# prints a small sample size warning.
WrapCOAST <- function(pheno) {
invisible(capture.output(
out <- COAST(
anno = anno,
geno = geno,
pheno = pheno,
is_pheno_binary = TRUE,
include_orig_skato_all = TRUE,
include_orig_skato_ptv = TRUE
)
))
return(out)
}
# Null phenotype.
p_omni <- WrapCOAST(null_pheno)
pvals <- p_omni@Pvals
p_omni <- as.numeric(pvals$pval[pvals$test == "omni"])
expect_gt(p_omni, 0.05)
# Alternative phenotype.
p_omni <- WrapCOAST(alt_pheno)
pvals <- p_omni@Pvals
p_omni <- as.numeric(pvals$pval[pvals$test == "omni"])
expect_equal(p_omni, 0.0, tolerance = 0.005)
})
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