tests/testthat/test-users.R

In lianos/sparrow: Take command of set enrichment analyses through a unified interface

context("Errors submitted by users")

test_that("seas fails with a 1-geneset GeneSetDb", {
  # Submitted by Thomas Sandmann:
  # https://github.com/lianos/multiGSEA/issues/7
  vm <- exampleExpressionSet()
  gdb <- exampleGeneSetDb()
  gdb <- gdb[geneSets(gdb)$name == 'GOZGIT_ESR1_TARGETS_DN']

  test.methods <- c("camera", "roast", "fry", "geneSetTest")
  mg <- seas(vm, gdb, test.methods, design = vm$design, contrast = 'tumor',
             ## customize camera parameter:
             inter.gene.cor = 0.04)

  # Calling the show,SparrowResult method is how this was identified,
  # so let's make sure that works, first.
  printed <- tryCatch(capture.output(show(mg)), error = function(e) NULL)
  expect_is(printed, "character")

  # Ensure that each method has an FDR/padj column
  for (method in test.methods) {
    res <- result(mg, method)
    expect_equal(nrow(res), 1L, info = method)
    expect_is(res[["padj"]], "numeric", info = method)
  }
})

test_that("seas pipeine can handle EList without a genes data.frame", {
  # Thanks to @RussBainer for reporting
  gdb <- exampleGeneSetDb()
  vm <- exampleExpressionSet()

  vm.noG <- vm
  vm.noG$genes <- NULL

  mg <- seas(vm, gdb, "camera", design = vm$design, contrast = "tumor")

  mg.noG <- expect_warning({
    seas(vm.noG, gdb, "camera", design = vm.noG$design, contrast = "tumor")
  }, "no.*genes", ignore.case = TRUE)

  r <- result(mg)
  r.noG <- result(mg.noG)
  expect_equal(r.noG, r)
})