tests/testthat/test-bugfixes.R

In seqMeta: Meta-Analysis of Region-Based Tests of Rare DNA Variants

context("other bug fixes")

data(seqMetaExample)

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# ISSUE N #
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## Template


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# ISSUE 3 #
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## Binomial imputation bug
test_that("imputation inside and outside the package get the same answer)", {
  Z <- Z1
  Z[1, 1] <- NA
  Zi <- Z
  Zi[1, 1] <- mean(Zi[ , 1], na.rm=TRUE)
  
  # binomial case
  expect_warning(so1b <- prepScores(Z=Z, ybin~sex+bmi, family=binomial(), SNPInfo=SNPInfo, data=pheno1))
  so2b <- prepScores(Z=Zi, ybin~sex+bmi, family=binomial(), SNPInfo=SNPInfo, data=pheno1)
  expect_equal(so1b, so2b)
  
  # gaussian case
  expect_warning(so1g <- prepScores(Z=Z, y~sex+bmi, SNPInfo=SNPInfo, data=pheno1))
  so2g <- prepScores(Z=Zi, y~sex+bmi, SNPInfo=SNPInfo, data=pheno1)
  expect_equal(so1g, so2g)
  
  # survival case
  expect_warning(so1c <- prepCox(Z=Z, Surv(time,status)~strata(sex)+bmi, SNPInfo=SNPInfo, data=pheno1))
  expect_warning(so2c <- prepCox(Z=Zi, Surv(time,status)~strata(sex)+bmi, SNPInfo=SNPInfo, data=pheno1))
  expect_equal(so1c, so2c)
  
  # [TBD: Male test cases] - imputation non-trivial as the implemented imputation is not transitive.
})

test_that("Verify the bug does not affect prepScores2)", {
  Z <- Z1
  Z[1, 1] <- NA
  Zi <- Z
  Zi[1, 1] <- mean(Zi[ , 1], na.rm=TRUE)
  
  # binomial case
  so1b <- prepScores2(Z=Z, ybin~sex+bmi, family="binomial", SNPInfo=SNPInfo, data=pheno1)
  so2b <- prepScores2(Z=Zi, ybin~sex+bmi, family="binomial", SNPInfo=SNPInfo, data=pheno1)
  expect_equal(so1b, so2b)
  
  # gaussian case
  so1g <- prepScores2(Z=Z, y~sex+bmi, SNPInfo=SNPInfo, data=pheno1)
  so2g <- prepScores2(Z=Zi, y~sex+bmi, SNPInfo=SNPInfo, data=pheno1)
  expect_equal(so1g, so2g)
  
  # survival case
  expect_warning(so1c <- prepScores2(Z=Z, Surv(time,status)~strata(sex)+bmi, family="cox", SNPInfo=SNPInfo, data=pheno1))
  expect_warning(so2c <- prepScores2(Z=Zi, Surv(time,status)~strata(sex)+bmi, family="cox", SNPInfo=SNPInfo, data=pheno1))
  expect_equal(so1c, so2c)
  
  # [TBD: Male test cases] - imputation non-trivial as the implemented imputation is not transitive.
})


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# ISSUE 2 #
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# test-issue2.R

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# ISSUE 1 #
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# test-issue1.R