tests/testthat/test_addKataegisIDtoVariants.R

In daanhazelaar/katdetectr: Detection, Characterization and Visualization of Kataegis in Sequencing Data

testthat::test_that("test .addKataegisIDtoVariants()", {

    # test on larger breast cancer sample
    genomicVariantsAnnotatedCPTAC <- system.file('extdata', 'CPTAC_Breast.vcf', package = 'katdetectr') |>
        .importGenomicVariants() |>
        .processGenomicVariants() |>
        .annotateGenomicVariants()
    changepointsCPTAC <- .performChangepointDetection(genomicVariantsAnnotated = genomicVariantsAnnotatedCPTAC, test.stat = "Exponential", penalty = "BIC", pen.value = 0, minseglen = 2, bpworkers = 1)
    segmentsCPTAC <- .annotateSegments(changepoints = changepointsCPTAC, genomicVariantsAnnotated = genomicVariantsAnnotatedCPTAC)
    kataegisFociCPTAC <- .determineKataegisFoci(segments = segmentsCPTAC, genomicVariantsAnnotated = genomicVariantsAnnotatedCPTAC, minSizeKataegis = 5, maxMeanIMD = 1000)
    genomicVariantsAnnotatedCPTACkat <- .addKataegisIDtoVariants(kataegisFoci = kataegisFociCPTAC, genomicVariantsAnnotated = genomicVariantsAnnotatedCPTAC)

    testthat::expect_equal(base::length(genomicVariantsAnnotatedCPTACkat), 3684)
    testthat::expect_equal(genomicVariantsAnnotatedCPTACkat$putativeKataegis[1], FALSE)
    testthat::expect_equal(genomicVariantsAnnotatedCPTACkat$putativeKataegis[363], TRUE)
    testthat::expect_equal(genomicVariantsAnnotatedCPTACkat$putativeKataegis[367], TRUE)
    testthat::expect_equal(genomicVariantsAnnotatedCPTACkat$putativeKataegis[368], FALSE)
    testthat::expect_equal(genomicVariantsAnnotatedCPTACkat$putativeKataegis[3138], FALSE)
    testthat::expect_equal(genomicVariantsAnnotatedCPTACkat$putativeKataegis[3139], TRUE)
    testthat::expect_equal(genomicVariantsAnnotatedCPTACkat$putativeKataegis[3157], TRUE)
    testthat::expect_equal(genomicVariantsAnnotatedCPTACkat$putativeKataegis[3158], FALSE)
})