tests/testthat/test-td.R

In yannchristinat/oncoscanR: Secondary analyses of CNV data (HRD and more)

test_that("TD score works - only gains, border checks", {
  cov <- GRanges(seqnames = factor(c(paste0(1:4, 'p'), paste0(1:4, 'q')),
                                   levels = c(paste0(1:4, 'p'), paste0(1:4, 'q'))),
                 ranges = IRanges(start = rep(1, 8),
                                  end = rep(200*10^6, 8)))
  segs <- GRanges(seqnames = factor(c(rep('1p', 5), rep('2p', 4)), levels = paste0(1:4, 'p')),
                  ranges = IRanges(start = c(1,   2,   3,  5, 20.000001, 50, 90.000001, 95, 100)*10^6 + 1,
                                   end =   c(1.1, 2.3, 4, 15, 30,        80, 91, 96.000001, 110.000001)*10^6),
                  cn = c(3, 4, 3, 4, 3, 4, 3, 4, 3),
                  cn.type = rep("Gain", 9))
  n <- score_td(segs)
  expected <- list(TDplus=3, TD=4)
  expect_equal(n, expected)
})

test_that("TD score works - CN checks", {
  cov <- GRanges(seqnames = factor(c(paste0(1:4, 'p'), paste0(1:4, 'q')),
                                   levels = c(paste0(1:4, 'p'), paste0(1:4, 'q'))),
                 ranges = IRanges(start = rep(1, 8),
                                  end = rep(200*10^6, 8)))
  segs <- GRanges(seqnames = factor(c(rep('1p', 7), rep('2p', 7)), levels = paste0(1:4, 'p')),
                  ranges = IRanges(start = rep(c(1,   10),7)*10^6 + 1,
                                   end =   rep(c(1.5, 15),7)*10^6),
                  cn = c(0,0,1,1,NA,NA,3,3,4,4,5,5,10,10),
                  cn.type = c("Loss", "Loss",
                              "Loss", "Loss",
                              "LOH", "LOH",
                              "Gain", "Gain",
                              "Gain", "Gain",
                              "Gain", "Gain",
                              "Gain", "Gain"))
  n <- score_td(segs)
  expected <- list(TDplus=2, TD=2)
  expect_equal(n, expected)
})

test_that("TD scores work - real case", {
  chas.fn <- system.file("extdata", "TDplus_gene_list_full_location.txt",
                         package = "oncoscanR")

  segments <- load_chas(chas.fn, oncoscanR::oncoscan_na33.cov)
  segs.clean <- trim_to_coverage(segments, oncoscanR::oncoscan_na33.cov) %>%
    prune_by_size()

  n <- score_td(segs.clean)
  expect_equal(n, list(TDplus=100, TD=22))  #Verified by hand in Excel and ChAS
})

test_that("TD scores work - empty segments", {
  segs <- GRanges(seqnames = factor(c(), levels = paste0(1:4, 'p')),
                  ranges = IRanges())
  n <- score_td(segs)
  expect_identical(unlist(n), c(TDplus=0,TD=0))
})