tests/testthat/test-annotate_fusion_calls.R

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

context("Test fusion annotation")

fusionfileArriba <- read_arriba_calls(system.file("extdata", "arriba_example.tsv", package = "annoFuseData"))

formattedArriba <-
  annoFuse::fusion_standardization(
    fusion_calls = fusionfileArriba,
    caller = "ARRIBA",
    tumorID = "BS_W97QQYKQ"
  )


fusionfileStarfusion <- read_starfusion_calls(system.file("extdata", "starfusion_example.tsv", package = "annoFuseData"))

formattedStarFusion <-
  annoFuse::fusion_standardization(
    fusion_calls = fusionfileStarfusion,
    caller = "STARFUSION",
    tumorID = "BS_W97QQYKQ"
  )

standardFusioncalls <- as.data.frame(rbind(formattedStarFusion, formattedArriba))

geneListReferenceDataTab <- read.delim(system.file("extdata", "genelistreference.txt", package = "annoFuseData"), stringsAsFactors = FALSE)

fusionReferenceDataTab <- read.delim(
  system.file("extdata", "fusionreference.txt", package = "annoFuseData"),
  stringsAsFactors = FALSE
)

filteredFusionAnnotated <- annotate_fusion_calls(
  standardFusioncalls = standardFusioncalls,
  geneListReferenceDataTab = geneListReferenceDataTab,
  fusionReferenceDataTab = fusionReferenceDataTab,
  checkReciprocal = TRUE
)

test_that("Standardizing arriba calls", {
  expect_equal(colnames(filteredFusionAnnotated), c("LeftBreakpoint", "RightBreakpoint", "FusionName", "Sample", "Caller", "Fusion_Type", "JunctionReadCount", "SpanningFragCount", "Confidence", "annots", "GeneA", "Gene1A", "Gene2A", "GeneB", "Gene1B", "Gene2B", "BreakpointLocation", "SpanningDelta", "reciprocal_exists", "Gene1A_anno", "Gene1B_anno", "Gene2A_anno", "Gene2B_anno", "Fusion_anno"))
  expect_equal(nrow(filteredFusionAnnotated), 26)
  expect_equal(unique(filteredFusionAnnotated$Sample), "BS_W97QQYKQ")
})