tests/testthat/test-merge_signatures.R

In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

context("test-merge_signatures")


# Get signatures
signatures <- get_known_signatures()

## Merge signatures
output <- merge_signatures(signatures)


## Merge signatures using a stricter cutoff
output_strict <- merge_signatures(signatures, cos_sim_cutoff = 0.9)

## Merge signatures using a different merging character
output_char <- merge_signatures(signatures, merge_char = "_")

# Tests
test_that("Output has correct class", {
  expect_true(inherits(output, "matrix"))
  expect_true(inherits(output_strict, "matrix"))
  expect_true(inherits(output_char, "matrix"))
})


test_that("Output sizes are correct", {
  expect_equal(dim(output), c(96, 43))
  expect_equal(dim(output_strict), c(96, 52))
  expect_equal(dim(output_char), c(96, 43))
})

test_that("Signature names are correct", {
  expect_equal(colnames(output), c(
    "SBS1", "SBS2", "SBS7a", "SBS7b", "SBS7c", "SBS7d", "SBS9",
    "SBS10a", "SBS10b", "SBS11", "SBS13", "SBS14", "SBS16", "SBS17a",
    "SBS17b", "SBS20", "SBS21", "SBS22", "SBS25", "SBS28", "SBS30",
    "SBS32", "SBS33", "SBS34", "SBS35", "SBS38", "SBS41",
    "SBS42", "SBS44", "SBS84", "SBS85", "SBS87", "SBS88",
    "SBS89", "SBS90", "SBS36;SBS18", "SBS15;SBS6", "SBS29;SBS24",
    "SBS40;SBS3;SBS5", "SBS8;SBS4", "SBS26;SBS12;SBS37", "SBS86;SBS39", "SBS23;SBS19;SBS31"
  ))
  expect_equal(colnames(output_strict), c(
    "SBS1", "SBS2", "SBS3", "SBS4", "SBS5", "SBS6", "SBS7a", "SBS7b",
    "SBS7c", "SBS7d", "SBS8", "SBS9", "SBS10a", "SBS10b", "SBS11",
    "SBS13", "SBS14", "SBS15", "SBS16", "SBS17a", "SBS17b", "SBS19",
    "SBS20", "SBS21", "SBS22", "SBS23", "SBS24", "SBS25", "SBS28",
    "SBS29", "SBS30", "SBS31", "SBS32", "SBS33", "SBS34", "SBS35",
    "SBS37", "SBS38", "SBS39", "SBS40", "SBS41", "SBS42", "SBS44",
    "SBS84", "SBS85", "SBS86", "SBS87", "SBS88", "SBS89", "SBS90",
    "SBS26;SBS12", "SBS36;SBS18"
  ))
  expect_equal(colnames(output_char), c(
    "SBS1", "SBS2", "SBS7a", "SBS7b", "SBS7c", "SBS7d", "SBS9",
    "SBS10a", "SBS10b", "SBS11", "SBS13", "SBS14", "SBS16", "SBS17a",
    "SBS17b", "SBS20", "SBS21", "SBS22", "SBS25", "SBS28", "SBS30",
    "SBS32", "SBS33", "SBS34", "SBS35", "SBS38", "SBS41",
    "SBS42", "SBS44", "SBS84", "SBS85", "SBS87", "SBS88",
    "SBS89", "SBS90", "SBS36_SBS18", "SBS15_SBS6", "SBS29_SBS24",
    "SBS40_SBS3_SBS5", "SBS8_SBS4", "SBS26_SBS12_SBS37", "SBS86_SBS39", "SBS23_SBS19_SBS31"
  ))
})

# Test that an error is given when the signature names already contain the merge_char
signatures_colnames <- signatures
colnames(signatures_colnames)[1] <- "SBS;1"
test_that("An error is given when signature names contain merge_char", {
  expect_error(
    {
      merge_signatures(signatures_colnames)
    },
    "Please remove all ; characters from your signature names."
  )
})