Nothing
context("cbind and rbind for scan1 objects")
grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
grav2 <- grav2[1:20,1:3]
map <- insert_pseudomarkers(grav2$gmap, step=1)
probs <- calc_genoprob(grav2, map, error_prob=0.002)
k <- calc_kinship(probs)
kloco <- calc_kinship(probs, "loco")
test_that("cbind.scan1() works for scan1() results", {
out1 <- scan1(probs, grav2$pheno[,1,drop=FALSE])
out2 <- scan1(probs, grav2$pheno[,2,drop=FALSE])
out12 <- scan1(probs, grav2$pheno[,1:2])
expect_equal(cbind(out1, out2), out12)
})
test_that("cbind.scan1() works for scan1/LMM results", {
out1 <- scan1(probs, grav2$pheno[,1,drop=FALSE], k)
out2 <- scan1(probs, grav2$pheno[,2,drop=FALSE], k)
out12 <- scan1(probs, grav2$pheno[,1:2], k)
expect_equal(cbind(out1, out2), out12, tolerance=1e-6)
out1 <- scan1(probs, grav2$pheno[,1,drop=FALSE], kloco)
out2 <- scan1(probs, grav2$pheno[,2,drop=FALSE], kloco)
out12 <- scan1(probs, grav2$pheno[,1:2], kloco)
expect_equal(cbind(out1, out2), out12, tolerance=1e-6)
})
test_that("rbind.scan1() works for scan1() results", {
skip_on_cran()
phe <- grav2$pheno[,1,drop=FALSE]
out1 <- scan1(probs[,1], phe)
out2 <- scan1(probs[,2:3], phe)
out3 <- scan1(probs[,3], phe)
out12 <- scan1(probs[,1:3], phe)
out123 <- scan1(probs[,c(1:3,3)], phe)
out2123 <- scan1(probs[,c(2:3,1,2:3,3)], phe)
expect_equal(rbind(out1, out2), out12)
expect_equal(rbind(out1, out2, out3), out123)
expect_equal(rbind(out2, out1, out2, out3), out2123)
})
test_that("rbind.scan1() works for scan1() results with multiple columns", {
skip_on_cran()
phe <- grav2$pheno[,15:18,drop=FALSE]
out1 <- scan1(probs[,1], phe)
out2 <- scan1(probs[,2:3], phe)
out3 <- scan1(probs[,3], phe)
out12 <- scan1(probs[,1:3], phe)
out123 <- scan1(probs[,c(1:3,3)], phe)
out2123 <- scan1(probs[,c(2:3,1,2:3,3)], phe)
expect_equal(rbind(out1, out2), out12)
expect_equal(rbind(out1, out2, out3), out123)
expect_equal(rbind(out2, out1, out2, out3), out2123)
})
test_that("rbind.scan1() works for scan1() results", {
skip_on_cran()
phe <- grav2$pheno[,1,drop=FALSE]
out1 <- scan1(probs[,1], phe, k)
out2 <- scan1(probs[,2:3], phe, k)
out3 <- scan1(probs[,3], phe, k)
out12 <- scan1(probs[,1:3], phe, k)
attr(out12, "hsq") <- rbind(attr(out1, "hsq"), attr(out2, "hsq")) # small adjustment
out123 <- scan1(probs[,c(1:3,3)], phe, k)
attr(out123, "hsq") <- rbind(attr(out1, "hsq"), attr(out2, "hsq"), attr(out3, "hsq")) # small adjustment
out2123 <- scan1(probs[,c(2:3,1,2:3,3)], phe, k)
attr(out2123, "hsq") <- rbind(attr(out2, "hsq"), attr(out1, "hsq"), attr(out2, "hsq"), attr(out3, "hsq")) # small adjustment
expect_equal(rbind(out1, out2), out12)
expect_equal(rbind(out1, out2, out3), out123)
expect_equal(rbind(out2, out1, out2, out3), out2123)
out1 <- scan1(probs[,1], phe, kloco[1])
out2 <- scan1(probs[,2:3], phe, kloco[2:3])
out3 <- scan1(probs[,3], phe, kloco[3])
out12 <- scan1(probs[,1:3], phe, kloco[1:3])
out123 <- scan1(probs[,c(1:3,3)], phe, kloco[c(1:3,3)])
out2123 <- scan1(probs[,c(2:3,1,2:3,3)], phe, kloco[c(2:3,1,2:3,3)])
expect_equal(rbind(out1, out2), out12)
expect_equal(rbind(out1, out2, out3), out123)
expect_equal(rbind(out2, out1, out2, out3), out2123)
})
test_that("rbind.scan1() works for scan1() results with multiple columns", {
skip_on_cran()
phe <- grav2$pheno[,15:18,drop=FALSE]
out1 <- scan1(probs[,1], phe, k)
out2 <- scan1(probs[,2:3], phe, k)
out3 <- scan1(probs[,3], phe, k)
out12 <- scan1(probs[,1:3], phe, k)
attr(out12, "hsq") <- rbind(attr(out1, "hsq"), attr(out2, "hsq")) # small adjustment
out123 <- scan1(probs[,c(1:3,3)], phe, k)
attr(out123, "hsq") <- rbind(attr(out1, "hsq"), attr(out2, "hsq"), attr(out3, "hsq")) # small adjustment
out2123 <- scan1(probs[,c(2:3,1,2:3,3)], phe, k)
attr(out2123, "hsq") <- rbind(attr(out2, "hsq"), attr(out1, "hsq"), attr(out2, "hsq"), attr(out3, "hsq")) # small adjustment
expect_equal(rbind(out1, out2), out12)
expect_equal(rbind(out1, out2, out3), out123)
expect_equal(rbind(out2, out1, out2, out3), out2123)
out1 <- scan1(probs[,1], phe, kloco[1])
out2 <- scan1(probs[,2:3], phe, kloco[2:3])
out3 <- scan1(probs[,3], phe, kloco[3])
out12 <- scan1(probs[,1:3], phe, kloco[1:3])
out123 <- scan1(probs[,c(1:3,3)], phe, kloco[c(1:3,3)])
out2123 <- scan1(probs[,c(2:3,1,2:3,3)], phe, kloco[c(2:3,1,2:3,3)])
expect_equal(rbind(out1, out2), out12)
expect_equal(rbind(out1, out2, out3), out123)
expect_equal(rbind(out2, out1, out2, out3), out2123)
})
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