context("prepScores2")
data(seqMetaExample)
test_that("prepScores2 equals prepScores (gaussian w/o family)", {
ps <- prepScores(Z=Z1, y~sex+bmi, SNPInfo=SNPInfo, data=pheno1)
ps2 <- prepScores2(Z=Z1, y~sex+bmi, family="gaussian", SNPInfo=SNPInfo, data=pheno1)
expect_equal(ps2, ps)
})
test_that("prepScores2 equals prepScores (gaussian w/ family)", {
ps <- prepScores(Z=Z2, y~sex+bmi, SNPInfo = SNPInfo, kins=kins, data=pheno2)
ps2 <- prepScores2(Z=Z2, y~sex+bmi, family="gaussian", SNPInfo=SNPInfo, kins=kins, data=pheno2)
expect_equal(ps2, ps)
})
test_that("prepScores2 equals prepScores (binomial)", {
ps <- prepScores(Z=Z1, ybin~1, family=binomial(), SNPInfo=SNPInfo, data=pheno1)
ps2 <- prepScores2(Z=Z1, ybin~1, family="binomial", SNPInfo=SNPInfo, data=pheno1)
expect_equal(ps2, ps)
})
# ###############
# ## SAME TESTS but for X
# ###############
test_that("prepScores2 equals prepScoresX (gaussian w/o family)", {
ps <- prepScoresX(Z=Z1, y~sex+bmi, male=pheno1$sex-1, SNPInfo=SNPInfo, data=pheno1)
ps2 <- prepScores2(Z=Z1, y~sex+bmi, male=pheno1$sex-1, family="gaussian", SNPInfo=SNPInfo, data=pheno1)
expect_equal(ps2, ps)
})
test_that("prepScores2 equals prepScoresX (gaussian w/ family)", {
ps <- prepScoresX(Z=Z2, y~sex+bmi, male=pheno2$sex-1, SNPInfo = SNPInfo, kins=kins, data=pheno2)
ps2 <- prepScores2(Z=Z2, y~sex+bmi, male=pheno2$sex-1, family="gaussian", SNPInfo=SNPInfo, kins=kins, data=pheno2)
expect_equal(ps2, ps)
})
test_that("prepScores2 equals prepScoresX (binomial)", {
ps <- prepScoresX(Z=Z1, ybin~1, male=pheno1$sex-1, family=binomial(), SNPInfo=SNPInfo, data=pheno1)
ps2 <- prepScores2(Z=Z1, ybin~1, male=pheno1$sex-1, family="binomial", SNPInfo=SNPInfo, data=pheno1)
expect_equal(ps2, ps)
})
###############
## SAME TESTS but for Survival
###############
test_that("prepScores2 equals prepCox", {
ps <- prepCox(Z=Z1, Surv(time,status)~strata(sex)+bmi, SNPInfo=SNPInfo, data=pheno1)
ps2 <- prepScores2(Z=Z1, Surv(time,status)~strata(sex)+bmi, family="cox", SNPInfo=SNPInfo, data=pheno1)
#prepCox stores the coxfit call in the attributes because it uses "by" instead of 'tapply'
expect_equal(ps2, ps, check.attributes=FALSE)
})
test_that("prepScores2 fails with incompatiple arguments", {
expect_error(prepScores2(Z=Z1, Surv(time,status)~strata(sex)+bmi, family="cox",
SNPInfo=SNPInfo, kins=kins, data=pheno1))
expect_error(prepScores2(Z=Z1, Surv(time,status)~strata(sex)+bmi, family="cox",
SNPInfo=SNPInfo, male=pheno1$sex-1, data=pheno1))
})
###############
## Missing values
###############
# test missing all missing genotypes in a snp gives the same as if the snp was removed from the genotype matrix
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.