tests/testthat/test_IsICAMSCatalog.R

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

context("Test IsICAMSCatalog function")

test_that("IsICAMSCatalog function", {
  skip_if("" == system.file(package = "BSgenome.Hsapiens.1000genomes.hs37d5"))
  dir <- c(system.file("extdata/Mutect-vcf",
                       package = "ICAMS"))
  catalogs <-
    VCFsToZipFile(dir,
                  zipfile = file.path(tempdir(), "test.zip"),
                  ref.genome = "hg19",
                  variant.caller = "mutect",
                  region = "genome",
                  base.filename = "Mutect")
  cat.sbs96 <- catalogs$catSBS96
  dim(cat.sbs96)
  expect_true(IsICAMSCatalog(cat.sbs96))
  
  # Test subsetting the catalog
  test <- cat.sbs96[, 1, drop = FALSE]
  dim(test)
  expect_true(IsICAMSCatalog(test)) 
  
  # Test a matrix with incorrect number of rows
  mat1 <- matrix(data = 1, nrow = 97)
  expect_false(IsICAMSCatalog(mat1)) 
  
  # Test a matrix with correct number of rows but incorrect class
  mat2 <- matrix(data = 1, nrow = 96)
  expect_false(IsICAMSCatalog(mat2)) 
  
  # Test a matrix with correct number of rows and class, but incorrect
  # rownames
  mat3 <- matrix(data = 1, nrow = 96)
  mat3 <- as.catalog(mat3, infer.rownames = TRUE)
  rownames(mat3) <- paste0("test", 1:96)
  
  result <- 
    expect_message(IsICAMSCatalog(mat3), 
                   "The rownames of the input object do not match the catalog row order used in ICAMS exactly.") 
  expect_false(result)
})