tests/testthat/test-zscored_annotation.R

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

context("Test zscore comparison 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
)

expressionMatrix <- readRDS(system.file("extdata", "expr_collapsed.rds", package = "annoFuseData"))
normData <- readRDS(system.file("extdata", "gtex_collapsed.rds", package = "annoFuseData"))
zscoredStandardFusioncalls <- zscored_annotation(standardFusioncalls,
  zscoreFilter = 2,
  normData = normData,
  expressionMatrix = expressionMatrix
)



test_that("Zscore comparison in standardized fusions", {
  expect_equal(colnames(zscoredStandardFusioncalls), c("FusionName", "Sample", "zscore_Gene1A", "zscore_Gene1B", "zscore_Gene2A", "zscore_Gene2B", "note_expression_Gene1A", "note_expression_Gene1B", "note_expression_Gene2A", "note_expression_Gene2B", "LeftBreakpoint", "RightBreakpoint", "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"))
})