tests/testthat/test-library.R

In athchen/PhIPData: Container for PhIP-Seq Experiments

context("Libraries can be stored and loaded for populating peptide information.")

test_that("libraries can be created", {
    # Test library creation
    virscan_file <- system.file("extdata", "virscan.tsv", package = "PhIPData")
    virscan_info <- readr::read_tsv(virscan_file,
        col_types = readr::cols(
            pep_id = readr::col_character(),
            pep_dna = readr::col_character(),
            pep_aa = readr::col_character(),
            pep_pos = readr::col_character(),
            pro_len = readr::col_double(),
            uniprot_acc = readr::col_character(),
            refseq = readr::col_character(),
            species = readr::col_character(),
            interspecies_specific = readr::col_character(),
            product = readr::col_character(),
            description = readr::col_character(),
            go = readr::col_character(),
            kegg = readr::col_character(),
            pfam = readr::col_character(),
            embl = readr::col_character(),
            interpro = readr::col_character(),
            pep_name = readr::col_character()
        )
    ) %>%
        as.data.frame()

    makeLibrary(virscan_info, "human")
    bfc <- BiocFileCache::BiocFileCache(
        tools::R_user_dir("beer", which = "cache"),
        ask = FALSE
    )

    libpath <- BiocFileCache::bfcquery(bfc, "library_human")
    expect_true(nrow(libpath) == 1)
})

test_that("Libraries can be accessed.", {
    # test use function
    n_samples <- 96L
    n_peptides <- nrow(virscan_info)
    counts <- matrix(sample(1:1e6, n_samples * n_peptides, replace = TRUE),
        nrow = n_peptides
    )
    logfc <- matrix(rnorm(n_samples * n_peptides, mean = 0, sd = 10),
        nrow = n_peptides
    )
    prob <- matrix(rbeta(n_samples * n_peptides, shape1 = 1, shape2 = 1),
        nrow = n_peptides
    )

    sampleInfo <- DataFrame(
        sample_name = paste0("sample", 1:n_samples),
        gender = sample(c("M", "F"), n_samples,
            replace = TRUE
        )
    )

    rownames(counts) <- rownames(logfc) <-
        rownames(prob) <- rownames(virscan_info) <-
        paste0("pep_", 1:n_peptides)

    colnames(counts) <- colnames(logfc) <-
        colnames(prob) <- rownames(sampleInfo) <-
        paste0("sample_", 1:n_samples)

    phip_obj <- PhIPData(
        counts = counts, logfc = logfc, prob = prob,
        sampleInfo = sampleInfo,
        peptideInfo = getLibrary("human")
    )

    expect_s4_class(phip_obj, "PhIPData")
})

test_that("Libraries can be removed", {
    # Test library removal functions
    removeLibrary("human")

    bfc <- BiocFileCache::BiocFileCache(
        tools::R_user_dir("beer", which = "cache"),
        ask = FALSE
    )
    libpath <- BiocFileCache::bfcquery(bfc, "library_human")
    expect_true(nrow(libpath) == 0)
})