context('Test output functions')
tmp <- './tmpdata'
simulation <- runSimulation(N=10, P=2, genVar=0.4, h2s=0.2, phi=0.8, delta=0.2)
genotypes <- simulation$rawComponents$genotypes
kinship <- simulation$rawComponents$kinship
phenotypes <- simulation$phenoComponentsFinal$Y
covariates <- simulation$phenoComponentsIntermediate$noiseFixed$cov
context('Test writeStandardOutput')
test_that('writeStandardOutput fails with missing output format', {
expect_error(writeStandardOutput(directory=tempdir(),
genotypes=genotypes$genotypes,
phenotypes=phenotypes,
id_samples = genotypes$id_samples,
id_snps = genotypes$id_snps,
id_phenos = colnames(phenotypes),
kinship=kinship),
"Output format has to be specified")
})
test_that('writeStandardOutput fails with path error', {
expect_error(writeStandardOutput(directory="~/test",
genotypes=genotypes$genotypes,
phenotypes=phenotypes,
id_samples = genotypes$id_samples,
id_snps = genotypes$id_snps,
id_phenos = colnames(phenotypes),
kinship=kinship,
format="plink"),
"directory contains ~:")
})
test_that('writeStandardOutput writes relevant plink files', {
write_out <- writeStandardOutput(directory=tmp,
genotypes=genotypes$genotypes,
phenotypes=phenotypes,
id_samples = genotypes$id_samples,
id_snps = genotypes$id_snps,
id_phenos = colnames(phenotypes),
kinship=kinship,
covariates=covariates,
format="plink", verbose=FALSE)
expect_true(file.exists(paste(tmp, "/Ysim_plink.txt", sep="")))
expect_true(file.exists(paste(tmp, "/Covs_plink.txt", sep="")))
expect_false(file.exists(paste(tmp, "/Kinship_plink.txt", sep="")))
expect_true(file.exists(paste(tmp, "/Genotypes.fam", sep="")))
expect_true(file.exists(paste(tmp, "/Genotypes.bim", sep="")))
expect_true(file.exists(paste(tmp, "/Genotypes.bed", sep="")))
})
test_that('writeStandardOutput writes relevant oxgen files', {
write_out <- writeStandardOutput(directory=tmp,
genotypes=genotypes$genotypes,
phenotypes=phenotypes,
id_samples = genotypes$id_samples,
id_snps = genotypes$id_snps,
id_phenos = colnames(phenotypes),
kinship=kinship,
covariates=covariates,
format="snptest", verbose=FALSE)
expect_true(file.exists(paste(tmp, "/Ysim_snptest.sample", sep="")))
expect_true(file.exists(paste(tmp, "/Genotypes_snptest.gen", sep="")))
expect_false(file.exists(paste(tmp, "/Kinship_snptest.txt", sep="")))
})
test_that('writeStandardOutput writes relevant gemma files', {
write_out <- writeStandardOutput(directory=tmp,
genotypes=genotypes$genotypes,
phenotypes=phenotypes,
id_samples = genotypes$id_samples,
id_snps = genotypes$id_snps,
id_phenos = colnames(phenotypes),
kinship=kinship,
covariates=covariates,
format="gemma", verbose=FALSE)
expect_true(file.exists(paste(tmp, "/Ysim_gemma.txt", sep="")))
expect_true(file.exists(paste(tmp, "/Kinship_gemma.txt", sep="")))
expect_true(file.exists(paste(tmp, "/Covs_gemma.txt", sep="")))
expect_true(file.exists(paste(tmp, "/Genotypes_gemma.txt", sep="")))
})
test_that('writeStandardOutput writes relevant bimbam files', {
write_out <- writeStandardOutput(directory=tmp,
genotypes=genotypes$genotypes,
phenotypes=phenotypes,
id_samples = genotypes$id_samples,
id_snps = genotypes$id_snps,
id_phenos = colnames(phenotypes),
kinship=kinship,
covariates=covariates,
format="bimbam", verbose=FALSE)
expect_true(file.exists(paste(tmp, "/Ysim_bimbam.txt", sep="")))
expect_false(file.exists(paste(tmp, "/Covs_bimbam.txt", sep="")))
expect_false(file.exists(paste(tmp, "/Kinship_bimbam.txt", sep="")))
expect_true(file.exists(paste(tmp, "/Genotypes_bimbam.csv", sep="")))
})
context('Test savePheno')
test_that('writeStandardOutput fails with path error', {
expect_error(savePheno(simulation, directory="~/fail",
outstring="Data_simulation", format=c("csv", "plink")),
"directory contains ~")
})
test_that('writeStandardOutput writes relevant main csv output', {
testdir <- savePheno(simulation, directory=tmp,
outstring="Data_simulation", format="csv",
saveIntermediate=FALSE,
verbose=FALSE)
expect_true(file.exists(paste(testdir, "/Ysim_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir, "/Y_genBg_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir, "/Y_genFixed_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir, "/Y_noiseBg_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir, "/Y_noiseFixed_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir, "/Genotypes_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir, "/SNP_NrSNP20_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir,
"/SNP_effects_NrSNP20_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir, "/Covs_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir, "/Covs_effect_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir, "/Kinship_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir, "/varComponents_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir, "/cov_noiseBg_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir, "/cov_genBg_Data_simulation.csv",
sep="")))
unlink(paste(testdir, "/*", sep=""))
})
test_that('writeStandardOutput writes additional csv output', {
testdir <- savePheno(simulation, directory=tmp,
outstring="Data_simulation", format="csv",
saveIntermediate=TRUE,
verbose=FALSE)
expect_true(file.exists(paste(testdir,
"/Y_genBg_independent_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_genBg_shared_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_genFixed_independent_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_genFixed_shared_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_noiseBg_independent_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_noiseBg_shared_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_noiseFixed_independent_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_noiseFixed_shared_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir,
"/cov_genBg_independent_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir,
"/cov_genBg_shared_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir,
"/cov_noiseBg_independent_Data_simulation.csv",
sep="")))
expect_true(file.exists(paste(testdir,
"/cov_noiseBg_shared_Data_simulation.csv",
sep="")))
unlink(paste(testdir, "/*", sep=""))
})
test_that('writeStandardOutput writes relevant main rds output', {
testdir <- savePheno(simulation, directory=tmp,
outstring="Data_simulation", format="rds",
saveIntermediate=FALSE,
verbose=FALSE)
expect_true(file.exists(paste(testdir, "/Ysim_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir, "/Y_genBg_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir, "/Y_genFixed_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir, "/Y_noiseBg_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir, "/Y_noiseFixed_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir, "/SNP_NrSNP20_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir,
"/SNP_effects_NrSNP20_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir, "/Covs_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir, "/Covs_effect_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir, "/Kinship_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir, "/varComponents_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir, "/cov_noiseBg_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir, "/cov_genBg_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir, "/Genotypes_Data_simulation.rds",
sep="")))
unlink(paste(testdir, "/*", sep=""))
})
test_that('writeStandardOutput writes additional rds output', {
testdir <- savePheno(simulation, directory=tmp,
outstring="Data_simulation", format="rds",
saveIntermediate=TRUE,
verbose=FALSE)
expect_true(file.exists(paste(testdir,
"/Y_genBg_independent_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_genBg_shared_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_genFixed_independent_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_genFixed_shared_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_noiseBg_independent_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_noiseBg_shared_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_noiseFixed_independent_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir,
"/Y_noiseFixed_shared_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir,
"/cov_genBg_independent_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir,
"/cov_genBg_shared_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir,
"/cov_noiseBg_independent_Data_simulation.rds",
sep="")))
expect_true(file.exists(paste(testdir,
"/cov_noiseBg_shared_Data_simulation.rds",
sep="")))
unlink(paste(testdir, "/*", sep=""))
})
unlink(paste(tmp, "/*", sep=""))
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