tests/testthat/test_getRegionsFromTxDb.R

In eisaR: Exon-Intron Split Analysis (EISA) in R

test_that("getRegionsFromTxDb() runs", {
    txdb <- AnnotationDbi::loadDb(system.file("extdata", "hg19sub.sqlite", package = "eisaR"))
    regL <- getRegionsFromTxDb(txdb)

    # arguments
    expect_error(getRegionsFromTxDb(1:10))
    expect_error(getRegionsFromTxDb(txdb, exonExt = "a"))
    expect_error(getRegionsFromTxDb(txdb, strandedData = "a"))

    # expected results
    expect_true(is.list(regL))
    expect_length(regL, 2L)
    expect_equivalent(lengths(regL), c(20L, 4L))
    expect_true(all(countOverlaps(regL$exons) == 1L))
    
    # same for EnsDb object
    # ... load GRanges with annotation (Y)
    load(system.file("YGRanges.RData", package="ensembldb"))
    # ... create EnsDb
    suppressWarnings(DB <- ensembldb::ensDbFromGRanges(Y, path=tempdir(), version=75,
                                                       organism="Homo_sapiens"))
    edb <- ensembldb::EnsDb(DB)
    # ... create corresponding TxDb
    suppressWarnings(txdb <- GenomicFeatures::makeTxDbFromGRanges(Y))
    # ... compare annotation
    expect_identical(length(GenomicFeatures::genes(edb)),
                     length(GenomicFeatures::genes(txdb)))
    expect_identical(length(GenomicFeatures::exons(edb)),
                     length(GenomicFeatures::exons(txdb)))
    # ... compare results
    regL1 <- getRegionsFromTxDb(edb)
    regL2 <- getRegionsFromTxDb(txdb)
    expect_identical(regL1, regL2)
})