tests/testthat/test-roxytest-testexamples-get_sig_similarity.R

In ShixiangWang/sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

# Generated by roxytest: do not edit by hand!

# File R/get_sig_similarity.R: @testexamples

test_that("Function get_sig_similarity() @ L102", {
  
  # Load mutational signature
  load(system.file("extdata", "toy_mutational_signature.RData",
    package = "sigminer", mustWork = TRUE
  ))
  
  s1 <- get_sig_similarity(sig2, Ref = sig2)
  s1
  
  s2 <- get_sig_similarity(sig2)
  s2
  s3 <- get_sig_similarity(sig2, sig_db = "SBS")
  s3
  
  # Set order for result similarity matrix
  s4 <- get_sig_similarity(sig2, sig_db = "SBS", set_order = TRUE)
  s4
  
  ## Remove some components
  ## in similarity calculation
  s5 <- get_sig_similarity(sig2,
    Ref = sig2,
    pattern_to_rm = c("T[T>G]C", "T[T>G]G", "T[T>G]T")
  )
  s5
  
  ## Same to DBS and ID signatures
  x1 <- get_sig_db("DBS_hg19")
  x2 <- get_sig_db("DBS_hg38")
  s6 <- get_sig_similarity(x1$db, x2$db)
  s6
  expect_equal(length(s1), 4L)
  expect_equal(length(s2), 4L)
  expect_equal(length(s3), 4L)
  expect_equal(length(s4), 4L)
  expect_equal(length(s5), 4L)
  expect_is(s6, "list")
})