tests/testthat/test-gene-rates.R

In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

# To generate test data for dndscv,
# run gene_mutation_rates(luad, covariates = "lung") with breakpoints before/after run_dndscv
# and save the input list and raw output to the .rds files. Also save the fit object, because
# a necessary component for generating it won't be saved with the raw output .rds.

test_that("gene mutation rates", {
  dndscv_cesa = load_cesa(get_test_file("luad_hg19_for_gene_rate_test.rds"))
  dndscv_input = get_test_data("dndscv_input_single.rds")
  dndscv_raw_output = get_test_data("dndscv_raw_output_single.rds")
  
  # Run gene_mutation_rates, but skip running dNdScv. Instead, verify that input to
  # run_dndscv matches what's expected, then load pre-generated output and continue
  dndscv_cesa = mockr::with_mock(
    run_dndscv = function(mutations, gene_list, cv, gr_genes, refdb) {
      expect_equal(list(mutations = mutations, gene_list = gene_list, cv = cv), dndscv_input)
      return(dndscv_raw_output)
    },
    get_dndscv_model_fit = function(dndscv_output) {
      return(get_test_data('dndscv_test_fit_object.rds'))
    },
    {
     gene_mutation_rates(dndscv_cesa, covariates = "lung")
    }
  )
  rates_ak = get_test_data("gene_mutation_rates_with_ci.rds")
  expect_equal(dndscv_cesa@mutrates, rates_ak)
  
})