tests/testthat/test_simulation.R

In CNPBayes: Bayesian mixture models for copy number polymorphisms

context("Simulation")

test_that("test_simulation", {
  set.seed(42)
  arguments <- list(sl.good = 6.25, sl.bad = 0.0625, prbias = 0.03,
                    n = 0.2, prvar = c(19.92985, 0.06272))
  dat <- simulateProbeLevel(cnvs = 1, K = 4, probes = 10,
                            arguments = arguments, qual = "medium")
  expect_identical(names(dat), c("measurements", "assignments"))
  if(FALSE){
    x <- dat[[1]]
    if (FALSE)
      hist(rowMeans(x[, , 1, 3]), col = "gray", breaks = 80)
    K <- 4
    xx <- x[, , 1, K]
    mns <- rowMeans(xx)
    pc <- prcomp(xx, center = TRUE, scale. = TRUE)$x[, 1]
    if (cor(pc, mns) < cor(-pc, mns)) {
      pc <- -pc
    }
    mp <- McmcParams(iter = 100, burnin = 10, nStarts = 1)
    mlist <- SingleBatchModelList(data=pc, k=1:4, mcmc.params=mp)
    mlist <- posteriorSimulation(mlist)
    m.y <- marginalLikelihood(mlist)
    expect_true(which.max(m.y) == 4L)
    if (FALSE){
      hist(pc, breaks = 100, col = "gray", border = "gray")
    }
  }
})