context("stepwiseqtl")
test_that("stepwiseqtl works with X-chr-specific perms", {
data(fake.f2)
fake.f2 <- calc.genoprob(fake.f2)
set.seed(17370120)
operm1 <- scantwopermhk(fake.f2, n.perm=10, verbose=FALSE)
set.seed(17370120)
operm2 <- scantwopermhk(fake.f2, n.perm=10, perm.Xsp=TRUE, verbose=FALSE)
pen1 <- calc.penalties(operm1)
pen2 <- calc.penalties(operm2)
out.sq1 <- stepwiseqtl(fake.f2, max.qtl=4, penalties=pen1, method="hk", verbose=FALSE)
expect_equal(out.sq1$chr, c("1", "8", "13", "X"))
expect_equal(out.sq1$pos, c(37.11, 61.20, 24.03, 14.20))
out.sq2 <- stepwiseqtl(fake.f2, max.qtl=4, penalties=pen2, method="hk", verbose=FALSE)
expect_equal(out.sq2$chr, c("1", "13", "X"))
expect_equal(out.sq2$pos, c(37.11, 24.03, 14.20))
out.sq3 <- stepwiseqtl(fake.f2, chr=1:19, max.qtl=4, penalties=pen2, method="hk", verbose=FALSE)
expect_equal(out.sq3$chr, c("1", "13"))
expect_equal(out.sq3$pos, c(37.11, 24.03))
pen2b <- calc.penalties(operm2, alpha=0.2)
out.sq2b <- stepwiseqtl(fake.f2, max.qtl=6, penalties=pen2b, method="hk", verbose=FALSE)
expect_equal(out.sq2b$chr, c("1", "8", "13", "X"))
expect_equal(out.sq2b$pos, c(37.11, 61.20, 24.03, 14.20))
})
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