library(bigsnpr)
gen <- function(n, m) {
I <- 1:m
p <- I / (2 * m + 1)
mat <- outer(I, I, FUN = function(i, j) {
1 / (abs(i - j) + 1)
})
bindata::rmvbin(n, p, bincorr = mat) +
bindata::rmvbin(n, p, bincorr = mat)
}
N <- 200
M <- 500
fake <- snp_fake(N, M)
G <- fake$genotypes
G[] <- rep(gen(N, M / 20), 20)
nbNA <- VGAM::rbetabinom.ab(M, size = N, shape1 = 0.6, shape2 = 20)
indNA <- cbind(
unlist(
lapply(nbNA, function(nb) {
`if`(nb > 0, sample(N, size = nb), NULL)
})
),
rep(cols_along(G), nbNA)
)
G[indNA] <- as.raw(3)
fake$map$chromosome <- sort(sample(1:2, M, TRUE))
snp_writeBed(fake, "inst/extdata/example-missing.bed")
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