context("add rsq")
load(system.file("extdata", "test_commondata.RData", package="TwoSampleMR"))
test_that("exposure data 1", {
# exp_dat <- extract_instruments("ieu-a-2")
d <- exp_dat %>% add_rsq()
expect_true("rsq.exposure" %in% names(d))
expect_true("effective_n.exposure" %in% names(d))
})
test_that("exposure data 2", {
skip("Skip unless you have good access to the API.")
d <- extract_instruments(c('ieu-a-2', 'ieu-a-7')) %>% add_rsq()
expect_true("rsq.exposure" %in% names(d))
expect_true("effective_n.exposure" %in% names(d))
})
exposure <- exp_dat[1:5,]
test_that("outcome data 1", {
skip("Skip unless you have good access to the API.")
d <- extract_outcome_data(exposure$SNP, 'ieu-a-2') %>% add_rsq()
expect_true("rsq.outcome" %in% names(d))
expect_true("effective_n.outcome" %in% names(d))
})
test_that("outcome data 2", {
skip("Skip unless you have good access to the API")
d <- extract_outcome_data(exposure$SNP, c('ieu-a-2', 'ieu-a-7')) %>% add_rsq()
expect_true("rsq.outcome" %in% names(d))
expect_true("effective_n.outcome" %in% names(d))
})
test_that("dat 2", {
skip("Skip unless you have good access to the API.")
d <- make_dat(proxies=FALSE) %>% add_rsq()
expect_true("rsq.outcome" %in% names(d) & "rsq.exposure" %in% names(d))
expect_true("effective_n.outcome" %in% names(d) & "effective_n.exposure" %in% names(d))
})
test_that("dat ukb-d", {
skip("Skip unless you have good access to the API.")
skip_on_ci()
skip_on_cran()
d <- make_dat(exposure="ukb-d-30710_irnt", proxies=FALSE) %>% add_rsq()
expect_true("rsq.outcome" %in% names(d) & "rsq.exposure" %in% names(d))
})
test_that("effective n", {
effn <- effective_n(c(1000, 20000), c(49000, 30000))
expect_true(
effn[1] < effn[2]
)
})
test_that("get_population_allele_frequency", {
skip("Skip unless you have good access to the API.")
d <- extract_instruments("ieu-a-7")
d <- add_metadata(d)
d$eaf.exposure.controls <- get_population_allele_frequency(
af = d$eaf.exposure,
prop = d$ncase.exposure / (d$ncase.exposure + d$ncontrol.exposure),
odds_ratio = exp(d$beta.exposure),
prevalence = 0.2
)
expect_equal(cor(d$eaf.exposure, d$eaf.exposure.controls), 1, tolerance = 0.1)
})
test_that("bbj-a-1", {
skip("Skip unless you have good access to the API.")
skip_on_ci()
skip_on_cran()
d <- extract_instruments('bbj-a-1') %>% add_metadata() %>% add_rsq()
expect_true(all(!is.na(d$rsq.exposure)))
})
test_that("bsen vs pn", {
skip("Skip unless you have good access to the API.")
d <- extract_instruments("ieu-a-2")
r1 <- get_r_from_bsen(d$beta.exposure, d$se.exposure, d$samplesize.exposure)
r2 <- get_r_from_pn(d$pval.exposure, d$samplesize.exposure)
expect_true(cor(abs(r1), r2) > 0.99)
})
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