Nothing
context("splatPopSimulate")
if (requireNamespace("VariantAnnotation", quietly = TRUE) &&
requireNamespace("preprocessCore", quietly = TRUE)) {
set.seed(1)
n.samples <- 6
n.genes <- 10
vcf <- mockVCF(n.samples = n.samples, n.snps = 1000)
params <- setParams(newSplatPopParams(), eqtl.n = 10, nGenes = n.genes)
}
test_that("splatPopSimulate output is valid and works", {
skip_if_not_installed("VariantAnnotation")
skip_if_not_installed("preprocessCore")
expect_true(validObject(splatPopSimulate(params = params, vcf = vcf)))
pop <- splatPopSimulateMeans(params = params, vcf = vcf)
expect_false(any(is.na(pop$means)))
expect_false(any(sapply(pop$means, is.infinite)))
expect_equal(ncol(pop$means), n.samples)
expect_length(pop$key, 15) # Number of columns expected in splatPop key
expect_true(validObject(splatPopSimulateSC(sim.means = pop$means,
key = pop$key,
params = params)))
})
test_that("splatPopSimulate on multiple groups output is valid and works", {
skip_if_not_installed("VariantAnnotation")
skip_if_not_installed("preprocessCore")
params.g2 <- setParams(params, group.prob = c(0.5, 0.5), nGenes = n.genes)
eqtl <- splatPopSimulate(params = params.g2, vcf = vcf)
expect_true(validObject(eqtl))
})
test_that("splatPopSimulate can read genes from gff data.frame", {
skip_if_not_installed("VariantAnnotation")
skip_if_not_installed("preprocessCore")
gff <- mockGFF(n.genes = n.genes)
sim <- splatPopSimulateMeans(vcf = vcf, params = params, gff = gff)
expect_true(validObject(sim))
})
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