tests/testthat/test-fusion_driver.R

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

context("Test fusion driver")

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

sfc <-
  annoFuse::fusion_standardization(
    fusion_calls = fusionfileArriba,
    caller = "ARRIBA",
    tumorID = "BS_W97QQYKQ"
  )
geneListReferenceDataTab <- read.delim(system.file("extdata", "genelistreference.txt", package = "annoFuseData"), stringsAsFactors = FALSE)
fusionReferenceDataTab <- read.delim(system.file("extdata", "fusionreference.txt", package = "annoFuseData"), stringsAsFactors = FALSE)

bioMartDataPfam <- readRDS(system.file("extdata", "pfamDataBioMart.RDS", package = "annoFuseData"))
kinaseid <- unique(bioMartDataPfam$pfam_id[grep("kinase", bioMartDataPfam$NAME)])
fusion_driver_df <- fusion_driver(sfc,
  annotated = FALSE,
  geneListReferenceDataTab = geneListReferenceDataTab,
  fusionReferenceDataTab = fusionReferenceDataTab,
  checkDomainStatus = TRUE,
  domainsToCheck = kinaseid
)


test_that("Fusion driver annotation for standardized arriba calls", {
  expect_equal(colnames(fusion_driver_df), c("LeftBreakpoint", "RightBreakpoint", "FusionName", "Sample", "Caller", "Fusion_Type", "JunctionReadCount", "SpanningFragCount", "Confidence", "annots", "GeneA", "Gene1A", "Gene2A", "GeneB", "Gene1B", "Gene2B", "BreakpointLocation", "SpanningDelta", "DomainRetainedGene1A", "DomainRetainedGene1B", "reciprocal_exists", "Gene1A_anno", "Gene1B_anno", "Gene2A_anno", "Gene2B_anno", "Fusion_anno"))
  expect_equal(nrow(fusion_driver_df), 5)
  expect_equal(fusion_driver_df$DomainRetainedGene1B[1], "Yes")
})