tests/testthat/test-ODER.R

In eolagbaju/ODER: Optimising the Definition of Expressed Regions

data(gtex_SRP012682_SRX222703_lung_auc_1, package = "ODER")
data(gtex_SRP012682_SRX222703_lung_ers_1, package = "ODER")

if (!exists("gtf_path")) {
    gtf_url <- paste0(
        "http://ftp.ensembl.org/pub/release-103/",
        "gtf/homo_sapiens/Homo_sapiens.GRCh38.103.chr.gtf.gz"
    )
    gtf_path <- file_cache(gtf_url)
}

if (!exists("gtf_grs")) {
    gtf_grs <- rtracklayer::import(gtf_path)
}

if (!exists("test_exons")) {
    test_exons <- get_exons(
        gtf = gtf_grs,
        ucsc_chr = TRUE,
        ignore.strand = TRUE
    )
}

if (!exists("test_ers_delta")) {
    test_ers_delta <- get_ers_delta(
        ers = gtex_SRP012682_SRX222703_lung_ers_1, # gtex_SRP012682_SRX222703_lung_ers_1 is from the data folder
        opt_exons = test_exons,
        delta_fun = .delta
    )
}

if (!exists("test_opt_ers")) {
    test_opt_ers <- get_opt_ers(
        ers = gtex_SRP012682_SRX222703_lung_ers_1,
        ers_delta = test_ers_delta
    )
}

if (!exists("rec_url")) {
    rec_url <- recount::download_study(
        project = "SRP012682",
        type = "samples",
        download = FALSE
    )
}

# don't test this on Windows
# ODER() -> get_coverage() -> derfinder::loadCoverage()
# which doesn't work on Windows due to rtracklayer version 1.25.16
if (!xfun::is_windows()) {
    bw_path <- ODER::file_cache(rec_url[1])

    test_ODER_opt_ers <- ODER(
        bw_paths = bw_path, auc_raw = gtex_SRP012682_SRX222703_lung_auc_1,
        auc_target = 40e6 * 100, chrs = c("chr21", "chr22"),
        genome = "hg38", mccs = c(5, 10), mrgs = c(10, 20),
        gtf = gtf_path, ucsc_chr = TRUE, ignore.strand = TRUE,
        exons_no_overlap = NULL, bw_chr = "chr"
    )

    test_ODER_strand_ers <- ODER(
        chrs = c("chr21", "chr22"), genome = "hg38", mccs = c(5, 10),
        mrgs = c(10, 20), gtf = gtf_path, ucsc_chr = TRUE, ignore.strand = TRUE,
        biotype = "Non-overlapping", bw_chr = "chr", file_type = "stranded",
        bw_pos = bw_path, bw_neg = bw_path, auc_target = 40e6 * 100,
        auc_raw_pos = gtex_SRP012682_SRX222703_lung_auc_1,
        auc_raw_neg = gtex_SRP012682_SRX222703_lung_auc_1
    )

    test_that("ODER works", {
        expect_error(ODER(
            bw_paths = bw_path, auc_raw = gtex_SRP012682_SRX222703_lung_auc_1,
            auc_target = 40e6 * 100, chrs = c("chr21", "chr22"),
            genome = "hg38", mccs = c(5, 10), mrgs = c(10, 20),
            gtf = NULL, ucsc_chr = TRUE, ignore.strand = TRUE,
            exons_no_overlap = NULL, bw_chr = "chr"
        ), "gtf must be provided.")
        expect_equal(test_opt_ers, test_ODER_opt_ers)
        expect_true(methods::is(test_ODER_opt_ers, "list"))
        expect_true(methods::is(test_ODER_opt_ers[[1]], "GenomicRanges"))
        expect_true(methods::is(test_ODER_opt_ers[[2]], "character"))
        expect_true(methods::is(test_ODER_opt_ers[[3]], "data.frame"))
        expect_equal(as.character(unique(BiocGenerics::strand(
            test_ODER_opt_ers[["opt_ers"]]
        ))), "*")
        expect_true(all(as.character(unique(strand(
            test_ODER_strand_ers[["opt_ers"]]
        ))) == c("+", "-")))
    })
}