tests/testthat/test_mvmr.R

In MRCIEU/TwoSampleMR: Two Sample MR Functions and Interface to MR Base Database

context("mvmr")

skip_on_cran()
skip_if_offline()
skip_if_offline(host = "api.opengwas.io")

test_that("control", {
	lipids <- try(mv_extract_exposures(c("ieu-a-299","ieu-a-300","ieu-a-302")))
	if (inherits(lipids, "try-error")) skip("Server issues")
	chd <- try(extract_outcome_data(lipids$SNP, "ieu-a-7"))
	if (inherits(chd, "try-error")) skip("Server issues")
	control <- try(mv_harmonise_data(lipids, chd))
	if (inherits(control, "try-error")) skip("Server issues")
	expect_output(print(mv_residual(control, intercept=TRUE, instrument_specific=TRUE)))
	expect_output(print(mv_residual(control, intercept=FALSE, instrument_specific=TRUE)))
	expect_output(print(mv_residual(control, intercept=TRUE, instrument_specific=FALSE)))
	expect_output(print(mv_residual(control, intercept=FALSE, instrument_specific=FALSE)))
	expect_output(print(mv_multiple(control, intercept=TRUE, instrument_specific=TRUE)))
	expect_output(print(mv_multiple(control, intercept=FALSE, instrument_specific=TRUE)))
	expect_output(print(mv_multiple(control, intercept=TRUE, instrument_specific=FALSE)))
	expect_output(print(mv_multiple(control, intercept=FALSE, instrument_specific=FALSE)))
})


test_that("dat", {
	a <- try(mv_extract_exposures(c("ukb-b-5238", "ieu-a-1001")))
	if (inherits(a, "try-error")) skip("Server issues")
	b <- try(extract_outcome_data(a$SNP, "ieu-a-297"))
	if (inherits(b, "try-error")) skip("Server issues")
	dat <- try(mv_harmonise_data(a, b))
	if (inherits(dat, "try-error")) skip("Server issues")
	expect_output(print(mv_residual(dat, intercept=TRUE, instrument_specific=TRUE)))
	expect_output(print(mv_residual(dat, intercept=FALSE, instrument_specific=TRUE)))
	expect_output(print(mv_residual(dat, intercept=TRUE, instrument_specific=FALSE)))
	expect_output(print(mv_residual(dat, intercept=FALSE, instrument_specific=FALSE)))
	expect_output(print(mv_multiple(dat, intercept=TRUE, instrument_specific=TRUE)))
	expect_output(print(mv_multiple(dat, intercept=FALSE, instrument_specific=TRUE)))
	expect_output(print(mv_multiple(dat, intercept=TRUE, instrument_specific=FALSE)))
	expect_output(print(mv_multiple(dat, intercept=FALSE, instrument_specific=FALSE)))
	expect_output(print(mv_ivw(dat)))
	expect_output(print(mv_basic(dat)))
})


test_that("ordering 1", {
	lipids1 <- try(mv_extract_exposures(c("ieu-a-299","ieu-a-300","ieu-a-302")))
	if (inherits(lipids1, "try-error")) skip("Server issues")
	chd1 <- try(extract_outcome_data(lipids1$SNP, "ieu-a-7"))
	if (inherits(chd1, "try-error")) skip("Server issues")
	control1 <- try(mv_harmonise_data(lipids1, chd1))
	if (inherits(control1, "try-error")) skip("Server issues")
	expect_output(print(mv_multiple(control1)))
})

test_that("ordering 2", {
	lipids2 <- try(mv_extract_exposures(c("ieu-a-302","ieu-a-300","ieu-a-299")))
	if (inherits(lipids2, "try-error")) skip("Server issues")
	chd2 <- try(extract_outcome_data(lipids2$SNP, "ieu-a-7"))
	if (inherits(chd2, "try-error")) skip("Server issues")
	control2 <- try(mv_harmonise_data(lipids2, chd2))
	if (inherits(control2, "try-error")) skip("Server issues")
	expect_output(print(mv_multiple(control2)))
})