tests/testthat/test_variants.r

In MRCIEU/ieugwasr: Interface to the 'OpenGWAS' Database API

# skip()
# skip_on_cran()
# skip_on_ci()


o1 <- variants_gene("ENSG00000123374")
if(inherits(o1, "response")) skip("Server issues")

o2 <- variants_gene("ENSG00000123374", 100000)

test_that("genes",
{
	expect_gt(nrow(o1), 0)
	expect_gt(nrow(o2), nrow(o1))
})


test_that("chrpos",
{
	o <- variants_chrpos("7:105561135-105563135")
	expect_true(nrow(o) > 1)

	o <- variants_chrpos("7:105561135")
	expect_true(nrow(o) == 1)

	o <- variants_chrpos("nonsense")
	expect_true(class(o) == "response")
})


test_that("rsid", 
{
	o <- variants_chrpos("7:105561135-105563135")
	p <- variants_rsid(o$name)
	expect_true(all(nrow(o) == nrow(p)))
	expect_true(all(o$name == p$name))
})


test_that("conversion",
{
	o <- variants_to_rsid(c("rs1205", "7:105561135"))
	expect_true(length(o) == 2)

	o <- variants_to_rsid(c("rs234", "7:105561135"))
	expect_true(length(o) == 1)

	o <- variants_to_rsid(c("rs234"))
	expect_true(length(o) == 1)
})