context("F1 genotyping")
test_that("get intuitive F1 genotyping", {
skip_on_os(os = "mac", arch = "aarch64")
load("testdat.RData")
ploidy <- 2
fout <- flexdog_full(refvec = refvec,
sizevec = sizevec,
ploidy = ploidy,
model = "f1",
p1ref = p1ref,
p1size = p1size,
p2ref = p2ref,
p2size = p2size)
expect_equal(fout$par$p1geno, 0)
expect_equal(fout$par$p2geno, 1)
})
test_that("flex_update_pivec gives intuitive results", {
skip_on_os(os = "mac", arch = "aarch64")
weight_vec <- c(70.87955, 64.10825, 0.01219)
control <- list(qarray = structure(c(1, 0.5, 0, 0.5, 0.25, 0, 0, 0, 0, 0,
0.5, 1, 0.5, 0.5, 0.5, 1, 0.5, 0, 0,
0, 0, 0, 0.25, 0.5, 0, 0.5, 1),
.Dim = c(3L, 3L, 3L),
.Dimnames = list(parent1 = c("aa", "Aa", "AA"),
parent2 = c("aa", "Aa", "AA"),
offspring = c("aa", "Aa", "AA"))),
fs1_alpha = 0.001,
outliers = FALSE,
pivec = c(0.501248485507885, 0.413481115690214, 0.0852703988019006),
p1_lbb = c(-0.0880572530585763, -26.8647138792035, -78.4850500935916),
p2_lbb = c(-40.6462413090379, -5.94237778106282, -54.0230897301435))
pout <- flex_update_pivec(weight_vec = weight_vec, model = "f1", control = control)
expect_equal(pout$par$p1geno, 0)
expect_equal(pout$par$p2geno, 1)
})
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