tests/testthat/test_makePhenotypes.R

In UKB.COVID19: UK Biobank COVID-19 Data Processing and Risk Factor Association Tests

test_that("Generate phenotypes",{
  
  phe <- makePhenotypes(ukb.data=covid_example("sim_ukb.tab.gz"),
                        res.eng=covid_example("sim_result_england.txt.gz"),
                        death.file=covid_example("sim_death.txt.gz"),
                        death.cause.file=covid_example("sim_death_cause.txt.gz"),
                        hesin.file=covid_example("sim_hesin.txt.gz"),
                        hesin_diag.file=covid_example("sim_hesin_diag.txt.gz"),
                        hesin_oper.file=covid_example("sim_hesin_oper.txt.gz"),
                        hesin_critical.file=covid_example("sim_hesin_critical.txt.gz"),
                        code.file=covid_example("coding240.txt.gz"),
                        pheno = "susceptibility")
  
  expect_s3_class( phe, "data.frame" )
  expect_equal( colnames(phe), c("ID", "pos.neg", "pos.ppl"))
  
})