context("basic HMM functions in risib")
test_that("risib nalleles works", {
expect_equal(nalleles("risib"), 2)
})
test_that("risib check_geno works", {
# autosome
expect_true(test_check_geno("risib", 0, TRUE, FALSE, FALSE, 0))
expect_true(test_check_geno("risib", 1, TRUE, FALSE, FALSE, 0))
expect_true(test_check_geno("risib", 2, TRUE, FALSE, FALSE, 0))
expect_true(test_check_geno("risib", 1, FALSE, FALSE, FALSE, 0))
expect_true(test_check_geno("risib", 2, FALSE, FALSE, FALSE, 0))
expect_false(test_check_geno("risib", 3, TRUE, FALSE, FALSE, 0))
expect_false(test_check_geno("risib", 0, FALSE, FALSE, FALSE, 0))
expect_false(test_check_geno("risib", 3, FALSE, FALSE, FALSE, 0))
# X chromosome
expect_true(test_check_geno("risib", 0, TRUE, TRUE, TRUE, 0))
expect_true(test_check_geno("risib", 1, TRUE, TRUE, TRUE, 0))
expect_true(test_check_geno("risib", 2, TRUE, TRUE, TRUE, 0))
expect_true(test_check_geno("risib", 1, FALSE, TRUE, TRUE, 0))
expect_true(test_check_geno("risib", 2, FALSE, TRUE, TRUE, 0))
expect_false(test_check_geno("risib", 3, TRUE, TRUE, TRUE, 0))
expect_false(test_check_geno("risib", 0, FALSE, TRUE, TRUE, 0))
expect_false(test_check_geno("risib", 3, FALSE, TRUE, TRUE, 0))
# X chr reverse
expect_true(test_check_geno("risib", 0, TRUE, TRUE, TRUE, 1))
expect_true(test_check_geno("risib", 1, TRUE, TRUE, TRUE, 1))
expect_true(test_check_geno("risib", 2, TRUE, TRUE, TRUE, 1))
expect_true(test_check_geno("risib", 1, FALSE, TRUE, TRUE, 1))
expect_true(test_check_geno("risib", 2, FALSE, TRUE, TRUE, 1))
expect_false(test_check_geno("risib", 3, TRUE, TRUE, TRUE, 1))
expect_false(test_check_geno("risib", 0, FALSE, TRUE, TRUE, 1))
expect_false(test_check_geno("risib", 3, FALSE, TRUE, TRUE, 1))
})
test_that("risib ngen works", {
expect_equal(test_ngen("risib", FALSE), 2)
expect_equal(test_ngen("risib", TRUE), 2)
})
test_that("risib possible_gen works", {
# autosome
expect_equal(test_possible_gen("risib", FALSE, FALSE, 0), 1:2)
# X chr
expect_equal(test_possible_gen("risib", TRUE, TRUE, 0), 1:2)
# X chr reverse
expect_equal(test_possible_gen("risib", TRUE, TRUE, 1), 1:2)
})
test_that("risib nrec works", {
# autosome
expect_equal(test_nrec("risib", 1, 1, FALSE, FALSE, 0), 0)
expect_equal(test_nrec("risib", 1, 2, FALSE, FALSE, 0), 1)
expect_equal(test_nrec("risib", 2, 1, FALSE, FALSE, 0), 1)
expect_equal(test_nrec("risib", 2, 2, FALSE, FALSE, 0), 0)
# X chr
expect_equal(test_nrec("risib", 1, 1, TRUE, TRUE, 0), 0)
expect_equal(test_nrec("risib", 1, 2, TRUE, TRUE, 0), 1)
expect_equal(test_nrec("risib", 2, 1, TRUE, TRUE, 0), 1)
expect_equal(test_nrec("risib", 2, 2, TRUE, TRUE, 0), 0)
# X chr reverse
expect_equal(test_nrec("risib", 1, 1, TRUE, TRUE, 1), 0)
expect_equal(test_nrec("risib", 1, 2, TRUE, TRUE, 1), 1)
expect_equal(test_nrec("risib", 2, 1, TRUE, TRUE, 1), 1)
expect_equal(test_nrec("risib", 2, 2, TRUE, TRUE, 1), 0)
})
test_that("risib init works", {
# autosome
expect_equal(test_init("risib", 1, FALSE, FALSE, 0), log(0.5))
expect_equal(test_init("risib", 2, FALSE, FALSE, 0), log(0.5))
# X chr
expect_equal(test_init("risib", 1, TRUE, TRUE, 0), log(2/3))
expect_equal(test_init("risib", 2, TRUE, TRUE, 0), log(1/3))
# X chr reverse
expect_equal(test_init("risib", 1, TRUE, TRUE, 1), log(1/3))
expect_equal(test_init("risib", 2, TRUE, TRUE, 1), log(2/3))
})
test_that("risib emit works", {
# autosome
eps <- 0.01
expect_equal(test_emit("risib", 0, 1, eps, integer(0), FALSE, FALSE, 0), 0)
expect_equal(test_emit("risib", 0, 2, eps, integer(0), FALSE, FALSE, 0), 0)
expect_equal(test_emit("risib", 1, 1, eps, integer(0), FALSE, FALSE, 0), log(1-eps))
expect_equal(test_emit("risib", 1, 2, eps, integer(0), FALSE, FALSE, 0), log(eps))
expect_equal(test_emit("risib", 2, 1, eps, integer(0), FALSE, FALSE, 0), log(eps))
expect_equal(test_emit("risib", 2, 2, eps, integer(0), FALSE, FALSE, 0), log(1-eps))
# X chr
expect_equal(test_emit("risib", 0, 1, eps, integer(0), TRUE, TRUE, 0), 0)
expect_equal(test_emit("risib", 0, 2, eps, integer(0), TRUE, TRUE, 0), 0)
expect_equal(test_emit("risib", 1, 1, eps, integer(0), TRUE, TRUE, 0), log(1-eps))
expect_equal(test_emit("risib", 1, 2, eps, integer(0), TRUE, TRUE, 0), log(eps))
expect_equal(test_emit("risib", 2, 1, eps, integer(0), TRUE, TRUE, 0), log(eps))
expect_equal(test_emit("risib", 2, 2, eps, integer(0), TRUE, TRUE, 0), log(1-eps))
# X chr reverse
expect_equal(test_emit("risib", 0, 1, eps, integer(0), TRUE, FALSE, 1), 0)
expect_equal(test_emit("risib", 0, 2, eps, integer(0), TRUE, FALSE, 1), 0)
expect_equal(test_emit("risib", 1, 1, eps, integer(0), TRUE, FALSE, 1), log(1-eps))
expect_equal(test_emit("risib", 1, 2, eps, integer(0), TRUE, FALSE, 1), log(eps))
expect_equal(test_emit("risib", 2, 1, eps, integer(0), TRUE, FALSE, 1), log(eps))
expect_equal(test_emit("risib", 2, 2, eps, integer(0), TRUE, FALSE, 1), log(1-eps))
# errors
expect_equal(test_emit("risib", 0, 0, eps, integer(0), FALSE, FALSE, 0), 0)
expect_equal(test_emit("risib", 0, 3, eps, integer(0), FALSE, FALSE, 0), 0)
expect_equal(test_emit("risib", 3, 1, eps, integer(0), FALSE, FALSE, 0), 0)
# X chr
expect_equal(test_emit("risib", 0, 0, eps, integer(0), TRUE, TRUE, 0), 0)
expect_equal(test_emit("risib", 0, 3, eps, integer(0), TRUE, TRUE, 0), 0)
expect_equal(test_emit("risib", 3, 1, eps, integer(0), TRUE, TRUE, 0), 0)
# X chr reverse
expect_equal(test_emit("risib", 0, 0, eps, integer(0), TRUE, FALSE, 1), 0)
expect_equal(test_emit("risib", 0, 3, eps, integer(0), TRUE, FALSE, 1), 0)
expect_equal(test_emit("risib", 3, 1, eps, integer(0), TRUE, FALSE, 1), 0)
})
test_that("risib step works", {
# autosome
rf <- 0.01
RF <- 4*rf/(1+6*rf)
expect_equal(test_step("risib", 1, 1, rf, FALSE, FALSE, 0), log(1-RF))
expect_equal(test_step("risib", 1, 2, rf, FALSE, FALSE, 0), log(RF))
expect_equal(test_step("risib", 2, 1, rf, FALSE, FALSE, 0), log(RF))
expect_equal(test_step("risib", 2, 2, rf, FALSE, FALSE, 0), log(1-RF))
# X chr (see table 3 in Broman, Genetics 169:1133-1146, 2005)
t11 <- (1+2*rf)/(1+4*rf)
t12 <- 2*rf/(1+4*rf)
t21 <- 4*rf/(1+4*rf)
t22 <- 1/(1+4*rf)
expect_equal(test_step("risib", 1, 1, rf, TRUE, TRUE, 0), log(t11))
expect_equal(test_step("risib", 1, 2, rf, TRUE, TRUE, 0), log(t12))
expect_equal(test_step("risib", 2, 1, rf, TRUE, TRUE, 0), log(t21))
expect_equal(test_step("risib", 2, 2, rf, TRUE, TRUE, 0), log(t22))
# X chr reverse
expect_equal(test_step("risib", 1, 1, rf, TRUE, FALSE, 1), log(t22))
expect_equal(test_step("risib", 1, 2, rf, TRUE, FALSE, 1), log(t21))
expect_equal(test_step("risib", 2, 1, rf, TRUE, FALSE, 1), log(t12))
expect_equal(test_step("risib", 2, 2, rf, TRUE, FALSE, 1), log(t11))
})
test_that("geno_names works", {
expect_equal(geno_names("risib", c("B", "R"), FALSE), c("BB", "RR"))
expect_equal(geno_names("risib", c("B", "R"), TRUE), c("BB", "RR"))
})
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