tests/testthat/test_prepare_elements.R

In reimandlab/ActiveDriverWGSR: A Driver Discovery Tool for Cancer Whole Genomes

context("Testing the prepare_elements_from_BED12 function")

test_that("Prepare Elements Imports Elements in the Correct Format", {

  elements = prepare_elements_from_BED12(system.file("extdata",
                                                     "chr17.coding_regions.bed",
                                                     package = "ActiveDriverWGS",
                                                     mustWork = TRUE))

  expect_is(elements, "data.frame")

  expect_equal(ncol(elements), 4)

  expect_is(elements[,1], "character")

  expect_is(elements[,2], "numeric")

  expect_is(elements[,3], "numeric")

  expect_is(elements[,4], "character")

  expect_identical(colnames(elements), c("chr", "start", "end", "id"))

  elements = prepare_elements_from_BED4(system.file("extdata",
                                                     "mini.ptm.bed",
                                                     package = "ActiveDriverWGS",
                                                     mustWork = TRUE))
  
  expect_is(elements, "data.frame")
  
  expect_equal(ncol(elements), 4)
  
  expect_is(elements[,1], "character")
  
  expect_is(elements[,2], "numeric")
  
  expect_is(elements[,3], "numeric")
  
  expect_is(elements[,4], "character")
  
  expect_identical(colnames(elements), c("chr", "start", "end", "id"))
})



test_that("Prepare Elements Throws the Right Errors",{

  # BED12
  expect_error(prepare_elements_from_BED12(
    system.file(
      "extdata",
      "cds_column_error.bed",
      package = "ActiveDriverWGS",
      mustWork = TRUE)),
      "Incorrect BED12 Format: 12 Columns in BED12 files")

  expect_error(prepare_elements_from_BED12(
    system.file(
      "extdata",
      "cds_str_coords_error.bed",
      package = "ActiveDriverWGS",
      mustWork = TRUE)),
    "Incorrect BED12 Format: Incorrect coordinate format")

  expect_error(prepare_elements_from_BED12(
    system.file(
      "extdata",
      "cds_chrom_error.bed",
      package = "ActiveDriverWGS",
      mustWork = TRUE)),
    "Incorrect BED12 Format: Chromosomes must be autosomal, sex or mitochondrial")

  expect_error(prepare_elements_from_BED12(
    system.file(
      "extdata",
      "cds_id_error.bed",
      package = "ActiveDriverWGS",
      mustWork = TRUE)),
    "Incorrect BED12 Format: IDs must be a character string")

  expect_error(prepare_elements_from_BED12(
    system.file(
      "extdata",
      "cds_blockcount_error.bed",
      package = "ActiveDriverWGS",
      mustWork = TRUE)),
    "Incorrect BED12 Format: Incorrect blockCounts")

  expect_error(prepare_elements_from_BED12(
    system.file(
      "extdata",
      "cds_blockstart_error.bed",
      package = "ActiveDriverWGS",
      mustWork = TRUE)),
    "Incorrect BED12 Format: Incorrect blockSizes or blockStarts")

  expect_error(prepare_elements_from_BED12(
    system.file(
      "extdata",
      "cds_blocksize_error.bed",
      package = "ActiveDriverWGS",
      mustWork = TRUE)),
    "Incorrect BED12 Format: Incorrect blockSizes or blockStarts")
  
  # BED4
  expect_error(prepare_elements_from_BED4(
    system.file(
      "extdata",
      "ptm_column_error.bed",
      package = "ActiveDriverWGS",
      mustWork = TRUE)),
    "Incorrect BED4 Format: 4 Columns in BED4 files")
  
  expect_error(prepare_elements_from_BED4(
    system.file(
      "extdata",
      "ptm_str_coords_error.bed",
      package = "ActiveDriverWGS",
      mustWork = TRUE)),
    "Incorrect BED4 Format: Incorrect coordinate format")
  
  expect_error(prepare_elements_from_BED4(
    system.file(
      "extdata",
      "ptm_chrom_error.bed",
      package = "ActiveDriverWGS",
      mustWork = TRUE)),
    "Incorrect BED4 Format: Chromosomes must be autosomal, sex or mitochondrial")
  
  expect_error(prepare_elements_from_BED4(
    system.file(
      "extdata",
      "ptm_id_error.bed",
      package = "ActiveDriverWGS",
      mustWork = TRUE)),
    "Incorrect BED4 Format: IDs must be a character string")
  

})