tests/testthat/test-get_coverage.R

In eolagbaju/ODER: Optimising the Definition of Expressed Regions

if (!exists("gtex_metadata")) {
    gtex_metadata <- recount::all_metadata("gtex")
    gtex_metadata <- gtex_metadata %>%
        as.data.frame() %>%
        dplyr::filter(project == "SRP012682")
}
if (!exists("rec_url")) {
    rec_url <- recount::download_study(
        project = "SRP012682",
        type = "samples",
        download = FALSE
    )
}
bw_path <- ODER::file_cache(rec_url[1])

bw_plus <- ODER::file_cache(rec_url[58])
bw_minus <- ODER::file_cache(rec_url[84])

data(gtex_SRP012682_SRX222703_lung_auc_1, package = "ODER")
data(gtex_SRP012682_SRX222703_lung_coverage_1, package = "ODER")
data(gtex_SRP012682_SRX222703_lung_ers_1, package = "ODER")

test_that("get_chr_info works", {
    chrs <- c("chr1", "chr2", "chr3")
    test_info <- get_chr_info(chrs = chrs, genome = "hg38")

    expect_false(test_info %contain% "chr4")
    expect_error(
        get_chr_info(
            chrs = "chromononsense",
            genome = "hg38"
        ),
        "Non-UCSC chromosome format was entered"
    )
    expect_equal(nrow(test_info), length(chrs))
    expect_type(test_info[["chrom"]], "character")
    expect_type(test_info[[2]], "integer")
    expect_type(test_info[[3]], "logical")
    expect_type(test_info[[4]], "logical")
})

test_that("get_coverage works", {
    expect_error(
        get_coverage(
            bw_paths = bw_path,
            auc_raw = "Not a number",
            auc_target = 40e6 * 100,
            chrs = c("chr21", "chr22")
        ),
        "Please enter a valid number for the auc values"
    )
    expect_error(
        get_coverage(
            bw_paths = bw_path,
            auc_raw = gtex_SRP012682_SRX222703_lung_auc_1, # gtex_SRP012682_SRX222703_lung_auc_1 is from the data folder
            auc_target = "Not a number",
            chrs = c("chr21", "chr22")
        ),
        "Please enter a valid number for the auc values"
    )
    expect_error(
        get_coverage(
            bw_paths = "",
            auc_raw = gtex_SRP012682_SRX222703_lung_auc_1,
            auc_target = 40e6 * 100,
            chrs = c("chr21", "chr22")
        ),
        "Please check your bigwig file paths are correct"
    )
    expect_error(
        get_coverage(
            auc_raw = gtex_SRP012682_SRX222703_lung_auc_1,
            auc_target = 40e6 * 100,
            chrs = c("chr21", "chr22")
        ),
        "bw_paths is empty"
    )

    expect_error(
        get_coverage(
            bw_paths = paste0(
                "~/.cache/BiocFileCache/25c6571687b_",
                "SRR660824_SRS389722_SRX222703_male_lung.png"
            ),
            auc_raw = gtex_SRP012682_SRX222703_lung_auc_1,
            auc_target = 40e6 * 100,
            chrs = c("chr21", "chr22")
        ),
        "Please check your bigwig file paths are correct"
    )
    expect_type(gtex_SRP012682_SRX222703_lung_coverage_1, "list") # gtex_SRP012682_SRX222703_lung_coverage_1 is from the data folder
    expect_type(gtex_SRP012682_SRX222703_lung_coverage_1[["chr21"]][["meanCoverage"]], "S4")
    expect_s4_class(gtex_SRP012682_SRX222703_lung_coverage_1[["chr21"]][["meanCoverage"]], "Rle")
    expect_equal(length(c("chr21", "chr22")), length(gtex_SRP012682_SRX222703_lung_coverage_1))
})

test_that("get_ers works", {
    test_er_df <- as.data.frame(gtex_SRP012682_SRX222703_lung_ers_1[[1]][[1]])

    expect_error(
        get_ers(
            mccs = c(5, 10),
            mrgs = c(10, 20)
        ),
        "Coverage is missing"
    )
    expect_error(
        get_ers(
            coverage = gtex_SRP012682_SRX222703_lung_coverage_1,
            mrgs = c(10, 20)
        ),
        "Mean Coverage Cutoff is empty"
    )
    expect_error(
        get_ers(
            coverage = gtex_SRP012682_SRX222703_lung_coverage_1,
            mccs = c(5, 10)
        ),
        "Max Region Gap is empty"
    )

    expect_type(gtex_SRP012682_SRX222703_lung_ers_1, "list") # gtex_SRP012682_SRX222703_lung_ers_1 is from the data folder
    expect_type(gtex_SRP012682_SRX222703_lung_ers_1[[1]][[1]], "S4")
    expect_s4_class(gtex_SRP012682_SRX222703_lung_ers_1[[1]][[1]], "GenomicRanges")
    expect_true(methods::is(test_er_df, "data.frame"))
})


# As of rtracklayer 1.25.16, BigWig is not supported on Windows.
if (!xfun::is_windows()) {
    test_strand_ers <- get_strand_ers(
        bw_pos = bw_plus, bw_neg = bw_minus, auc_raw_pos = gtex_metadata[["auc"]][58],
        auc_raw_neg = gtex_metadata[["auc"]][84], auc_target = 40e6 * 100,
        chrs = "chr21", mccs = c(5, 10), mrgs = c(10, 20), bw_chr = "chr"
    )
    test_that("get_strand_ers works", {
        expect_true("+" %in% unlist(as.list(BiocGenerics::strand(test_strand_ers[[1]][[1]]))))
        expect_true("-" %in% unlist(as.list(BiocGenerics::strand(test_strand_ers[[1]][[1]]))))
        expect_false("*" %in% unlist(as.list(BiocGenerics::strand(test_strand_ers[[1]][[1]]))))
    })
}