tests/testthat/test-count_dbs_contexts.R

In UMCUGenetics/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

context("test-count_dbs_contexts")

## Get a GRangesList object with dbs contexts.
grl_dbs_context <- readRDS(system.file("states/blood_grl_dbs_context.rds",
  package = "MutationalPatterns"
))

output <- count_dbs_contexts(grl_dbs_context)
expected <- readRDS(system.file("states/blood_dbs_counts.rds",
  package = "MutationalPatterns"
))

test_that("Output has correct class", {
  expect_true(inherits(output, c("matrix")))
})

test_that("Output is identical to expected", {
  expect_identical(output, expected)
})


grl_dbs_context_bad <- readRDS(system.file("states/blood_grl_dbs.rds",
                                        package = "MutationalPatterns"
))


test_that("An error occurs when the context has not been set.", {
    expect_error({count_dbs_contexts(grl_dbs_context_bad)},
                 "There are some REF or ALT bases, that do not belong")
    })