tests/testthat/test-DGEList.R

In facileverse/FacileBioc: FacileData API wrappers over Bioconductor assay containers.

context("DGEList")

if (!exists("Y")) Y <- NULL
if (!exists("dlist")) dlist <- example_bioc_data("DGEList", y = Y)

test_that("facilitate.DGEList works", {
  f <- facilitate(dlist)

  expect_setequal(names(f), names(dlist))
  expect_s4_class(f, "FacileDGEList")
  expect_s4_class(f, "FacileBiocDataStore")
  expect_s4_class(f, "FacileDataStore")
  expect_s4_class(f, "DGEList")
  checkmate::expect_list(ifacile(f))

  covs <- samples(f) |>
    with_sample_covariates("sex") |>
    with_sample_covariates("sample_type")
  expect_s3_class(covs, "facile_frame")
  expect_equal(nrow(covs), unname(ncol(f)))
  checkmate::expect_factor(covs[["sex"]], c("m", "f"))
  checkmate::expect_factor(covs[["sample_type"]], c("normal", "tumor"))

  expect_s4_class(fds(covs), "FacileDGEList")
})

test_that("alternate assay use for facilitated DGEList", {
  yx <- example_bioc_data("DGEList")
  yf <- facilitate(yx)

  cdata <- yf |>
    fetch_assay_data(
      rownames(yx)[1:2],
      assay_name = "counts",
      normalized = FALSE) |>
    with_sample_covariates(c("sex", "sample_type"))

  adata <- yf |>
    fetch_assay_data(
      rownames(yx)[1:2],
      assay_name = "atenth",
      normalized = FALSE) |>
    with_sample_covariates(c("sex", "sample_type"))
  expect_equal(adata$value, cdata$value / 10)
})