tests/testthat/test_otherformats.R

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

context("other formats")

# dat <- make_dat("ieu-a-2", "ieu-a-7")
load(system.file("extdata", "test_commondata.RData", package="TwoSampleMR"))


test_that("MRInput", {
	skip_if(getRversion() < '4.4.0') # because MendelianRandomization will not be installed
	w <- dat_to_MRInput(dat, get_correlations=FALSE)
	expect_true(length(w) == 1)
	expect_true(class(w) == "list")
	expect_true(class(w[[1]]) == "MRInput")
})

test_that("MRInput with cor", {
  skip_on_cran()
  skip_if_offline()
  skip_if_offline(host = "api.opengwas.io")
  skip_if(getRversion() < '4.4.0') # because MendelianRandomization will not be installed
	w <- tryCatch(dat_to_MRInput(dat, get_correlations=TRUE)[[1]],
	              error = skip("Server issues"),
	              warning = expect_warning())
	expect_true(nrow(w@correlation) == length(w@betaX))
})


test_that("mrpresso", {
	expect_warning(w <- run_mr_presso(dat))
	expect_true(length(w) == 1)
	expect_true(class(w) == "list")
	expect_true(class(w[[1]]) == "list")
	expect_true(length(w[[1]]) == 2)
})


test_that("radial MR dat", {
	w <- dat_to_RadialMR(dat)
	expect_true(class(w) == "list")
	expect_true(nrow(w[[1]]) == nrow(dat))
})


test_that("radial MR", {
	w <- dat_to_RadialMR(dat)
	expect_warning(o <- RadialMR::ivw_radial(w[[1]]))
	expect_true(class(o) == "IVW")
})


test_that("radial MR", {
	w <- mr_ivw_radial(dat$beta.exposure, dat$beta.outcome, dat$se.exposure, dat$se.outcome)
	expect_true(class(w) == "list")
})