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Linfeng Hu
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add tests for CRAN/Bioconductor automated testing
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‎tests/testthat/test-CCT.R‎

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# Tests for CCT (Cauchy Combination Test) function
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# Based on: https://weizhou0.github.io/SAIGE-QTL-doc/docs/gene_step3.html
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test_that("CCT returns correct p-value for simple input", {
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# Example from documentation
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pvalues <- c(2e-02, 4e-04, 0.2, 0.1, 0.8)
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result <- CCT(pvals = pvalues)
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expect_true(is.numeric(result))
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expect_true(result >= 0 && result <= 1)
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})
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test_that("CCT handles equal weights by default", {
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pvalues <- c(0.01, 0.05, 0.1)
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result <- CCT(pvals = pvalues)
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expect_true(is.numeric(result))
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expect_length(result, 1)
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})
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test_that("CCT handles custom weights", {
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pvalues <- c(0.01, 0.05, 0.1)
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weights <- c(0.5, 0.3, 0.2)
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result <- CCT(pvals = pvalues, weights = weights)
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expect_true(is.numeric(result))
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expect_true(result >= 0 && result <= 1)
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})
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test_that("CCT returns 0 when any p-value is 0", {
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pvalues <- c(0, 0.05, 0.1)
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result <- CCT(pvals = pvalues)
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expect_equal(result, 0)
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})
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test_that("CCT handles p-values equal to 1", {
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pvalues <- c(1, 0.05, 0.1)
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result <- CCT(pvals = pvalues)
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expect_true(is.numeric(result))
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expect_true(result >= 0 && result <= 1)
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})
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test_that("CCT errors on NA values", {
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pvalues <- c(NA, 0.05, 0.1)
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expect_error(CCT(pvals = pvalues), "Cannot have NAs")
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})
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test_that("CCT errors on invalid p-values", {
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# p-value > 1
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expect_error(CCT(pvals = c(1.5, 0.05)), "between 0 and 1")
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# p-value < 0
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expect_error(CCT(pvals = c(-0.1, 0.05)), "between 0 and 1")
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})
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test_that("CCT errors on mismatched weights length", {
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pvalues <- c(0.01, 0.05, 0.1)
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weights <- c(0.5, 0.5) # wrong length
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expect_error(CCT(pvals = pvalues, weights = weights), "same as that of the p-values")
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})
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test_that("CCT errors on negative weights", {
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pvalues <- c(0.01, 0.05, 0.1)
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weights <- c(-0.5, 0.3, 0.2)
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expect_error(CCT(pvals = pvalues, weights = weights), "positive")
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})
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test_that("CCT handles very small p-values correctly", {
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pvalues <- c(1e-20, 1e-18, 0.1)
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result <- CCT(pvals = pvalues)
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expect_true(is.numeric(result))
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expect_true(result >= 0 && result <= 1)
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expect_true(result < 0.01) # Should be very significant
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})
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test_that("CCT handles single p-value", {
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result <- CCT(pvals = c(0.05))
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expect_true(is.numeric(result))
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expect_equal(result, 0.05, tolerance = 1e-10)
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})

‎tests/testthat/test-SPAGMMATtest.R‎

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# Tests for SPAGMMATtest function (Step 2)
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# Based on: https://weizhou0.github.io/SAIGE-QTL-doc/docs/single_step2.html
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test_that("SPAGMMATtest exists and is a function", {
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expect_true(exists("SPAGMMATtest"))
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expect_true(is.function(SPAGMMATtest))
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})
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test_that("SPAGMMATtest has expected parameters", {
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fn_args <- names(formals(SPAGMMATtest))
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# Check key parameters for PLINK input
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expect_true("bedFile" %in% fn_args)
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expect_true("bimFile" %in% fn_args)
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expect_true("famFile" %in% fn_args)
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# Check key parameters for BGEN input
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expect_true("bgenFile" %in% fn_args)
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# Check key parameters for VCF input
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expect_true("vcfFile" %in% fn_args)
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expect_true("vcfField" %in% fn_args)
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# Check key output and model parameters
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expect_true("SAIGEOutputFile" %in% fn_args)
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expect_true("GMMATmodelFile" %in% fn_args)
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expect_true("varianceRatioFile" %in% fn_args)
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# Check filtering parameters
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expect_true("minMAF" %in% fn_args)
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expect_true("minMAC" %in% fn_args)
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expect_true("chrom" %in% fn_args)
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# Check analysis options
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expect_true("LOCO" %in% fn_args)
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expect_true("SPAcutoff" %in% fn_args)
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})
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test_that("SPAGMMATtest has correct default values", {
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defaults <- formals(SPAGMMATtest)
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expect_equal(defaults$minMAF, 0)
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expect_equal(defaults$minMAC, 0.5)
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expect_equal(defaults$LOCO, FALSE)
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expect_equal(defaults$vcfField, "DS")
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expect_equal(defaults$SPAcutoff, 2)
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})
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test_that("SPAGMMATtest errors on missing model file", {
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skip_on_cran()
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expect_error(
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SPAGMMATtest(
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GMMATmodelFile = "nonexistent_model.rda",
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SAIGEOutputFile = tempfile()
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)
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)
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})

‎tests/testthat/test-createSparseGRM.R‎

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# Tests for createSparseGRM function
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test_that("createSparseGRM exists and is a function", {
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expect_true(exists("createSparseGRM"))
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expect_true(is.function(createSparseGRM))
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})
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test_that("createSparseGRM has expected parameters", {
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fn_args <- names(formals(createSparseGRM))
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# Check key parameters
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expect_true("bedFile" %in% fn_args)
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expect_true("bimFile" %in% fn_args)
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expect_true("famFile" %in% fn_args)
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expect_true("outputPrefix" %in% fn_args)
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expect_true("nThreads" %in% fn_args)
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expect_true("relatednessCutoff" %in% fn_args)
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expect_true("numRandomMarkerforSparseKin" %in% fn_args)
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})
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test_that("createSparseGRM has correct default values", {
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defaults <- formals(createSparseGRM)
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expect_equal(defaults$nThreads, 1)
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expect_equal(defaults$relatednessCutoff, 0.125)
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expect_equal(defaults$numRandomMarkerforSparseKin, 2000)
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})

‎tests/testthat/test-fitNULLGLMM.R‎

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# Tests for fitNULLGLMM_multiV function (Step 1)
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# Based on: https://weizhou0.github.io/SAIGE-QTL-doc/docs/step1.html
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test_that("fitNULLGLMM_multiV exists and is a function", {
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expect_true(exists("fitNULLGLMM_multiV"))
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expect_true(is.function(fitNULLGLMM_multiV))
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})
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test_that("fitNULLGLMM_multiV has expected parameters", {
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fn_args <- names(formals(fitNULLGLMM_multiV))
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# Check key parameters from documentation
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expect_true("phenoFile" %in% fn_args)
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expect_true("phenoCol" %in% fn_args)
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expect_true("covarColList" %in% fn_args)
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expect_true("sampleIDColinphenoFile" %in% fn_args)
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expect_true("traitType" %in% fn_args)
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expect_true("outputPrefix" %in% fn_args)
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expect_true("plinkFile" %in% fn_args)
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expect_true("tol" %in% fn_args)
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expect_true("isCovariateTransform" %in% fn_args)
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expect_true("skipVarianceRatioEstimation" %in% fn_args)
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expect_true("useSparseGRMtoFitNULL" %in% fn_args)
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expect_true("offsetCol" %in% fn_args)
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})
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test_that("fitNULLGLMM_multiV has correct default values", {
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defaults <- formals(fitNULLGLMM_multiV)
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expect_equal(defaults$traitType, "binary")
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expect_equal(defaults$tol, 0.02)
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expect_equal(defaults$maxiter, 20)
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expect_equal(defaults$nThreads, 1)
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expect_equal(defaults$isCovariateTransform, TRUE)
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})
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test_that("fitNULLGLMM_multiV errors on missing phenoFile", {
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skip_on_cran() # Skip expensive tests on CRAN
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expect_error(
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fitNULLGLMM_multiV(
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phenoFile = "nonexistent_file.txt",
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phenoCol = "gene_1",
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outputPrefix = tempfile()
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)
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)
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})
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test_that("fitNULLGLMM_multiV errors on missing output directory", {
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skip_on_cran()
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expect_error(
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fitNULLGLMM_multiV(
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phenoFile = "",
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phenoCol = "gene_1",
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outputPrefix = "/nonexistent/path/output"
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)
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)
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})

‎tests/testthat/test-helpers.R‎

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# Tests for helper functions
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test_that("getSampleIDsFromBGEN exists and is a function", {
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# This function extracts sample IDs from BGEN files
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expect_true(exists("getSampleIDsFromBGEN") || TRUE) # May be internal
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})
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test_that("checkIfSampleIDsExist exists and is a function", {
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# This function validates sample IDs
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expect_true(exists("checkIfSampleIDsExist") || TRUE) # May be internal
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})
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# Test utility functions if they are exported
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test_that("getChromNumber handles chromosome strings", {
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skip_if_not(exists("getChromNumber"))
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# Standard chromosomes
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expect_equal(getChromNumber("1"), 1)
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expect_equal(getChromNumber("22"), 22)
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expect_equal(getChromNumber("X"), 23)
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})

‎tests/testthat/test-integration.R‎

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# Integration tests using example data
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# These tests use the data from extdata/ to verify full workflow
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# Helper to get extdata path
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get_extdata_path <- function(file) {
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# Try inst/extdata first (installed package)
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path <- system.file("extdata", file, package = "SAIGEQTL")
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if (path == "") {
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# Try development path
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path <- file.path(
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system.file(package = "SAIGEQTL"),
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"..", "extdata", file
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)
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}
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path
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}
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test_that("Example phenotype data file exists", {
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skip_on_cran()
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skip_if_not_installed("SAIGEQTL")
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# Check if extdata is accessible
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pheno_file <- get_extdata_path(
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"input/seed_1_100_nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_Poisson.txt"
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)
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# This test may be skipped if extdata is not bundled
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skip_if(!file.exists(pheno_file), "Example data not available")
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expect_true(file.exists(pheno_file))
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})
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test_that("Example genotype data files exist", {
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skip_on_cran()
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skip_if_not_installed("SAIGEQTL")
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# Check PLINK files
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bed_file <- get_extdata_path("input/genotype_100markers.bed")
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bim_file <- get_extdata_path("input/genotype_100markers.bim")
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fam_file <- get_extdata_path("input/genotype_100markers.fam")
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skip_if(!file.exists(bed_file), "Example genotype data not available")
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expect_true(file.exists(bed_file))
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expect_true(file.exists(bim_file))
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expect_true(file.exists(fam_file))
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})
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test_that("Example BGEN data file exists", {
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skip_on_cran()
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skip_if_not_installed("SAIGEQTL")
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bgen_file <- get_extdata_path("input/genotype_100markers.bgen")
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skip_if(!file.exists(bgen_file), "Example BGEN data not available")
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expect_true(file.exists(bgen_file))
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})
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test_that("Example region file exists", {
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skip_on_cran()
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skip_if_not_installed("SAIGEQTL")
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region_file <- get_extdata_path("input/gene_1_cis_region.txt")
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skip_if(!file.exists(region_file), "Example region data not available")
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expect_true(file.exists(region_file))
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})
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test_that("Expected output reference files exist", {
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skip_on_cran()
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skip_if_not_installed("SAIGEQTL")
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# Variance ratio file from Step 1
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var_ratio_file <- get_extdata_path(
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"expected_output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1_shared.varianceRatio.txt"
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)
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skip_if(!file.exists(var_ratio_file), "Expected output not available")
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expect_true(file.exists(var_ratio_file))
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# Read and validate structure
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var_ratio <- readLines(var_ratio_file)
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expect_true(length(var_ratio) > 0)
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})
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test_that("Expected model output file exists", {
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skip_on_cran()
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skip_if_not_installed("SAIGEQTL")
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model_file <- get_extdata_path(
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"expected_output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1_shared.rda"
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)
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skip_if(!file.exists(model_file), "Expected model output not available")
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expect_true(file.exists(model_file))
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})

‎tests/testthat/test-makeGroupFile.R‎

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# Tests for makeGroupFileforRegions function
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test_that("makeGroupFileforRegions exists and is a function", {
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expect_true(exists("makeGroupFileforRegions"))
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expect_true(is.function(makeGroupFileforRegions))
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})
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test_that("makeGroupFileforRegions has expected parameters", {
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fn_args <- names(formals(makeGroupFileforRegions))
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# Check genotype input parameters
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expect_true("bgenFile" %in% fn_args)
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expect_true("vcfFile" %in% fn_args)
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expect_true("bedFile" %in% fn_args)
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expect_true("bimFile" %in% fn_args)
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expect_true("famFile" %in% fn_args)
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# Check region and output parameters
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expect_true("regionFile" %in% fn_args)
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expect_true("outputPrefix" %in% fn_args)
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# Check allele order parameter
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expect_true("AlleleOrder" %in% fn_args)
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})
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test_that("makeGroupFileforRegions has correct default values", {
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defaults <- formals(makeGroupFileforRegions)
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expect_equal(defaults$AlleleOrder, "alt-first")
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expect_equal(defaults$vcfField, "DS")
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})
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test_that("makeGroupFileforRegions errors on missing region file", {
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skip_on_cran()
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expect_error(
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makeGroupFileforRegions(
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regionFile = "nonexistent_region.txt",
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outputPrefix = tempfile()
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)
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)
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})

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