tests/testthat/test_CollapseCatalog.R

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

context("CollapseCatalog")

test_that("Collapse1536CatalogTo96 block 1", {
  skip_if("" == system.file(package = "BSgenome.Hsapiens.1000genomes.hs37d5"))
  stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5"))
  cat.SBS1536 <-
    ReadCatalog("testdata/regress.cat.sbs.1536.csv", ref.genome = "GRCh37",
                region = "genome", catalog.type = "counts")
  x1 <- Collapse1536CatalogTo96(cat.SBS1536)
  expect_equal(colSums(cat.SBS1536), colSums(x1))
  expect_equal("SBS96Catalog", class(x1)[1])

  cat.SBS1536.density <-
    TransformCatalog(cat.SBS1536, target.ref.genome = "GRCh37",
                     target.region = "genome",
                     target.catalog.type = "density")
  x2 <- Collapse1536CatalogTo96(cat.SBS1536.density)
  expect_equal(colSums(cat.SBS1536.density), colSums(x2))
  expect_equal("SBS96Catalog", class(x2)[1])

  cat.SBS1536.counts.signature <-
    TransformCatalog(cat.SBS1536, target.ref.genome = "GRCh37",
                     target.region = "genome",
                     target.catalog.type = "counts.signature")
  x3 <- Collapse1536CatalogTo96(cat.SBS1536.counts.signature)
  expect_equal(colSums(cat.SBS1536.counts.signature), colSums(x3))
  expect_equal("SBS96Catalog", class(x3)[1])

  cat.SBS1536.density.signature <-
    TransformCatalog(cat.SBS1536, target.ref.genome = "GRCh37",
                     target.region = "genome",
                     target.catalog.type = "density.signature")
  x4 <- Collapse1536CatalogTo96(cat.SBS1536.density.signature)
  expect_equal(colSums(cat.SBS1536.density.signature), colSums(x4))
  expect_equal("SBS96Catalog", class(x4)[1])
})

test_that("Collapse192CatalogTo96 block 2", {
  skip_if("" == system.file(package = "BSgenome.Hsapiens.1000genomes.hs37d5"))
  stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5"))
  cat.SBS192 <-
    ReadCatalog("testdata/regress.cat.sbs.192.csv", ref.genome = "GRCh37",
                region = "transcript", catalog.type = "counts")
  x1 <- Collapse192CatalogTo96(cat.SBS192)
  expect_equal(colSums(cat.SBS192), colSums(x1))
  expect_equal("SBS96Catalog", class(x1)[1])

  cat.SBS192.density <-
    TransformCatalog(cat.SBS192, target.ref.genome = "GRCh37",
                     target.region = "transcript",
                     target.catalog.type = "density")
  x2 <- Collapse192CatalogTo96(cat.SBS192.density)
  expect_equal(colSums(cat.SBS192.density), colSums(x2))
  expect_equal("SBS96Catalog", class(x2)[1])

  cat.SBS192.counts.signature <-
    TransformCatalog(cat.SBS192, target.ref.genome = "GRCh37",
                     target.region = "transcript",
                     target.catalog.type = "counts.signature")
  x3 <- Collapse192CatalogTo96(cat.SBS192.counts.signature)
  expect_equal(colSums(cat.SBS192.counts.signature), colSums(x3))
  expect_equal("SBS96Catalog", class(x3)[1])

  cat.SBS192.density.signature <-
    TransformCatalog(cat.SBS192, target.ref.genome = "GRCh37",
                     target.region = "transcript",
                     target.catalog.type = "density.signature")
  x4 <- Collapse192CatalogTo96(cat.SBS192.density.signature)
  expect_equal(colSums(cat.SBS192.density.signature), colSums(x4))
  expect_equal("SBS96Catalog", class(x4)[1])
})

test_that("Collapse144CatalogTo78", {
  skip_if("" == system.file(package = "BSgenome.Hsapiens.1000genomes.hs37d5"))
  stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5"))
  cat.DBS144 <-
    ReadCatalog("testdata/regress.cat.dbs.144.csv", ref.genome = "GRCh37",
                region = "transcript", catalog.type = "counts")
  x1 <- Collapse144CatalogTo78(cat.DBS144)
  expect_equal(colSums(cat.DBS144), colSums(x1))
  expect_equal("DBS78Catalog", class(x1)[1])

  cat.DBS144.density <-
    TransformCatalog(cat.DBS144, target.ref.genome = "GRCh37",
                     target.region = "transcript",
                     target.catalog.type = "density")
  x2 <- Collapse144CatalogTo78(cat.DBS144.density)
  expect_equal(colSums(cat.DBS144.density), colSums(x2))
  expect_equal("DBS78Catalog", class(x2)[1])

  cat.DBS144.counts.signature <-
    TransformCatalog(cat.DBS144, target.ref.genome = "GRCh37",
                     target.region = "transcript",
                     target.catalog.type = "counts.signature")
  x3 <- Collapse144CatalogTo78(cat.DBS144.counts.signature)
  expect_equal(colSums(cat.DBS144.counts.signature), colSums(x3))
  expect_equal("DBS78Catalog", class(x3)[1])

  cat.DBS144.density.signature <-
    TransformCatalog(cat.DBS144, target.ref.genome = "GRCh37",
                     target.region = "transcript",
                     target.catalog.type = "density.signature")
  x4 <- Collapse144CatalogTo78(cat.DBS144.density.signature)
  expect_equal(colSums(cat.DBS144.density.signature), colSums(x4))
  expect_equal("DBS78Catalog", class(x4)[1])
})