tests/testthat/test_get_beta_value.R

In markgene/yamatClassifier: Yet Another Methylation Array Toolkit: Classifier

context("Test get_beta()")
library(yamatClassifier)


test_that("get_beta()", {
  idat_dir <- file.path(system.file("extdata", package = "minfiData"), "5723646052")
  targets <- data.frame(
    Basename = c(
      "5723646052_R02C02",
      "5723646052_R04C01",
      "5723646052_R05C02"
    ),
    Sentrix_ID = "5723646052"
  )
  trainer <- yamatClassifier::create_trainer(idat_dir = idat_dir,
                                             targets = targets,
                                             output = "output/5723646052")
  unmeth <- yamatClassifier::get_beta_value(trainer = trainer)
  expect_true(file.exists("output/5723646052/beta_value.Rda"))
  expect_equal(nrow(unmeth), 360456)
  expect_equal(ncol(unmeth), 3)
})