tests/testthat/test-aggregate_fusion_calls.R

In d3b-center/annoFuse: annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

context("Test aggregate fusion calls")

standardFusioncalls <- standardFusioncalls <- annoFuse::annoFuse_single_sample(
  # Example files are provided in extdata, at-least 1 fusionfile is required along
  # with its rsem expression file
  fusionfileArriba = system.file("extdata", "arriba_example.tsv", package = "annoFuseData"),
  fusionfileStarFusion = system.file("extdata", "starfusion_example.tsv", package = "annoFuseData"),
  expressionFile = system.file("extdata", "example.rsem.genes.results.gz", package = "annoFuseData"),
  tumorID = "BS_W97QQYKQ",
  # multiple read flag values for filtering using FusionAnnotator values
  artifactFilter = "GTEx_Recurrent|DGD_PARALOGS|Normal|BodyMap|ConjoinG",
  # keep all in-frame , frameshift and other types of Fusion_Type
  readingFrameFilter = "in-frame|frameshift|other",
  # keep all fusions with atleast 1 junction read support
  junctionReadCountFilter = 1,
  # keep only fusions where spanningFragCount-junctionReadCountFilter less than equal to 10
  spanningFragCountFilter = 10,
  # keep read throughs
  readthroughFilter = FALSE
)

aggregate_fusion_calls_out <- aggregate_fusion_calls(standardFusioncalls)

test_that("Aggregate fusion calls output from non-empty arriba and starfusion fusion calls", {
  expect_equal(
    colnames(aggregate_fusion_calls_out),
    c(
      "LeftBreakpoint", "RightBreakpoint", "FusionName", "Sample", "Caller", "Fusion_Type",
      "JunctionReadCount", "SpanningFragCount", "Confidence", "annots", "Gene1A", "Gene2A",
      "Gene1B", "Gene2B", "BreakpointLocation", "SpanningDelta", "reciprocal_exists",
      "Gene1A_anno", "Gene1B_anno", "Gene2A_anno", "Gene2B_anno", "Fusion_anno",
      "CalledBy", "caller_count"
    )
  )
  expect_equal(aggregate_fusion_calls_out[21, "caller_count"], 2)
})

test_that("keep only in-frame and frameshift fusions", {
  afc_noother <- aggregate_fusion_calls(standardFusioncalls, removeother = TRUE)
  dim(afc_noother)
  expect_equal(nrow(afc_noother), 9)
})