tests/testthat/test-loadAnnot.R

In BIMSBbioinfo/ciRcus: Annotation, analysis and visualization of circRNA data

test_that("summarizeCircs", {


  circ.files <- list.files(system.file("extdata/encode_demo_small",
                                       package = "ciRcus"),
                           pattern = "sites.bed",
                           full.names = TRUE)

  se <- summarizeCircs(circ.files, wobble = 1, keepCols = 1:7)

  # score matrix should be 4 by 6 (4 circs, 6 samples)
  expect_equal(dim(assays(se)$circ),     c(4, 6))
  # there should be 4 assays
  expect_equal(length(assays(se)), 4)
  # the total number of circRNA reads in FrontalCortex rep1 should be 1574
  expect_equal(sum(assays(se)$circ[, 1]),  1574)
  # circ read counts
  expect_equal(assays(se)$circ[[3, 3]],     14892)
  expect_equal(unname(colSums(assays(se)$circ)),
               c(1574, 757, 17266, 7221, 67, 93))
  # lin read counts
  expect_equal(assays(se)$linear.start[[3, 3]], 2362)
  # lin read count for a non-existing circRNA
  expect_equal(assays(se)$linear.end[[2, 1]], 90)
  # circular unique read counts
  expect_equal(unname(rowSums(assays(se)$circ.uniq)), c(1105, 40, 4866, 218))
  # resTable tests
  expect_equal(dim(resTable(se)), c(4, 29))

})


test_that("Annotation", {

  circ.files <- list.files(system.file("extdata/encode_demo_small",
                                       package = "ciRcus"),
                           pattern = "sites.bed",
                           full.names = TRUE)

  se <- summarizeCircs(circ.files, wobble = 1, keepCols = 1:7)

  # load annotation
  annot.file <- system.file("extdata/db/hsa_ens75_minimal.sqlite",
                            package = "ciRcus")
  annot.list <- loadAnnotation(annot.file)

  se.annot <- annotateCircs(se = se, annot.list = annot.list, assembly = "hg19")

  # annotation tests, separate functions
  se <- annotateHostGenes(se, annot.list$genes)
  expect_equal(resTable(se)$gene_id, c("ENSG00000183023",
                                       "ENSG00000183023",
                                       "ENSG00000183023",
                                       "ENSG00000180357"))
  se <- annotateFlanks(se, annot.list$gene.feats)
  expect_equal(resTable(se)$feature[2], "utr5:cds")
  expect_equal(resTable(se)$feature[4], "utr5:cds")
  se <- annotateJunctions(se, annot.list$junctions)
  expect_equal(resTable(se)$junct.known, c("5pr", "5pr", "5pr", "both"))
  se <- circLinRatio(se)
  expect_equal(unname(assays(se)$ratio[3, 4]), 4.03)
  expect_equal(unname(assays(se)$ratio[2, 3]), 0.04)

  # annotation test, wrapper, should behave the same as separate tests
  expect_equal(resTable(se.annot)$feature[2], "utr5:cds")
  expect_equal(resTable(se.annot)$feature[4], "utr5:cds")
  expect_equal(resTable(se.annot)$junct.known, c("5pr", "5pr", "5pr", "both"))
  expect_equal(unname(assays(se.annot)$ratio[3, 4]), 4.03)
  expect_equal(resTable(se.annot)$gene_id, c("ENSG00000183023",
                                             "ENSG00000183023",
                                             "ENSG00000183023",
                                             "ENSG00000180357"))

})

test_that("sample labels are robust upon resorting colData", {

  circ.files <- list.files(system.file("extdata/encode_demo_small",
                                       package = "ciRcus"),
                           pattern = "sites.bed",
                           full.names = TRUE)


  se.sorted   <- summarizeCircs(circ.files,      wobble = 1, keepCols = 1:7)
  se.unsorted <- summarizeCircs(rev(circ.files), wobble = 1, keepCols = 1:7)

  # rownames should be equal to sample column
  expect_equal(rownames(colData(se.sorted)),   colData(se.sorted)$sample)
  expect_equal(rownames(colData(se.unsorted)), colData(se.unsorted)$sample)

  # sorted vs. sorted
  expect_equal(unname(assays(se.sorted)$circ[, "FrontalCortex_rep1_sites.bed"]),
               resTable(se.sorted)[["FrontalCortex_rep1_sites.bed_circ"]])
  # unsorted vs. unsorted
  expect_equal(unname(assays(se.unsorted)$circ[,
                                               "FrontalCortex_rep1_sites.bed"]),
               resTable(se.unsorted)[["FrontalCortex_rep1_sites.bed_circ"]])

  # sorted vs. unsorted, assays()
  expect_equal(assays(se.sorted)$circ[, "FrontalCortex_rep1_sites.bed"],
               assays(se.unsorted)$circ[, "FrontalCortex_rep1_sites.bed"])
  # sorted vs. unsorted, resTable()
  expect_equal(resTable(se.sorted)[, "FrontalCortex_rep1_sites.bed_circ"],
               resTable(se.unsorted)[, "FrontalCortex_rep1_sites.bed_circ"])
})

test_that("CIRI2 input can be digested by ciRcus", {

  circ.files <- list.files(system.file("extdata/ciri_demo_hek",
                                       package = "ciRcus"),
                           pattern = "HEK",
                           full.names = TRUE)

  se <- summarizeCircs(circ.files, keep.linear = FALSE, wobble = 1,
                       subs = "all", qualfilter = FALSE, keepCols = 1:12)

  # total circRNAs in both samples
  expect_equal(nrow(resTable(se)), 14936)
  # there should be 4127 ribozero circRNAs
  expect_equal(
    sum(resTable(se)[, "HEK_riborezo_CIRI_sites.txt_circ"] > 0), 4127)
  # there should be 14013 RNaseR circRNAs
  expect_equal(
    sum(resTable(se)[, "HEK_RNaseR_CIRI_sites.txt_circ"] > 0), 14013)
})