tests/testthat/test-classifiers.R

In coregenomics/nascentrna: Classify Nascent RNA Transcripts using Decision Tree

context("test-classifiers.R")

test_that("da_tss returns all valid hits", {
    result <- da_tss(tss, genes)
    ## Count hits.
    expect_equal(length(result), length(idx_da_tss))
    ## Check distances.
    expect_equal(mcols(result)$distance, dist_da_tss)
    ## Check from-to (# nolint) mapping.
    expected <- Hits(from = idx_da_tss,
                     to = rep(1:2, each = 3),
                     nLnode = length(tss),
                     nRnode = length(genes),
                     distance = dist_da_tss)
    expect_equal(expected, result)
})

test_that("da_tss validates that genes do not overlap", {
    expect_error(da_tss(tss, genes_overlapping), "overlap")
})

test_that("da_tss validates min parameter", {
    expect_error(da_tss(tss, genes, min = 400, max = 300), "min")
})

test_that("ua_rna returns all valid hits", {
    result <- ua_rna(tss, genes)
    ## count hits.
    expect_equal(length(result), length(idx_ua_rna))
    ## Check distances.
    expect_equal(mcols(result)$distance, dist_ua_rna)
    ## Check from-to (# nolint) mapping.
    expected <- Hits(from = idx_ua_rna,
                     to = 1:2,
                     nLnode = length(tss),
                     nRnode = length(genes),
                     distance = dist_ua_rna)
    expect_equal(expected, result)
})

test_that("enhancer validates tre strandedness", {
    BiocGenerics::strand(tre[2]) <- "-"
    expect_error(enhancer(tre, genes), "strand")
    BiocGenerics::strand(tre[2]) <- "+"
    expect_error(enhancer(tre, genes), "strand")
})

test_that("enhancer subsets valid GRanges", {
    result <- enhancer(tre, genes)
    expected <- tre[idx_enhancer]
    expect_equal(expected, result)
})

test_that("annotate classifies all features", {
    result <- annotate(tss, genes)
    is_da_tss <- mcols(result)$class %in% "daTSS"
    expect_equal(sum(is_da_tss), length(idx_da_tss))
    expect_equal(which(is_da_tss), idx_da_tss)
})