tests/testthat/test-all_genes.R

In neurogenomics/orthogene: Interspecies gene mapping

test_that("all_genes works", {
    n_genes <- function(dat) {
        length(unique(dat$Gene.Symbol))
    }
    ##### Test function ####
    run_tests <- function(method) {
        genome_human <- all_genes(
            species = "human",
            method = method
        )
        genome_mouse <- all_genes(
            species = "mouse",
            method = method
        )
        genome_zebrafish <- all_genes(
            species = "zebrafish",
            method = method
        )
        genome_fly <- all_genes(
            species = "fly",
            method = method
        )
        #### Test human ####
        expected_human <- if (method == "gprofiler") 35000 else 19000
        testthat::expect_gte(
            n_genes(genome_human),
            expected_human
        )
        #### Test mouse ####
        expected_mouse <- if (method == "gprofiler") 50000 else 21000
        testthat::expect_gte(
            n_genes(genome_mouse),
            expected_mouse
        )
        #### Test zebrafish ####
        expected_zebrafish <- if (method == "gprofiler") 25000 else 20000
        testthat::expect_gte(
            n_genes(genome_zebrafish),
            expected_zebrafish
        )
        #### Test fly ####
        expected_fly <- if (method == "gprofiler") 4000 else 8000
        testthat::expect_gte(
            n_genes(genome_fly),
            expected_fly
        )
    }

    # Fly is the only species tested here that gprofiler
    # does worse on.
    ##### gprofiler tests ####
    # run_tests(method = "gprofiler") # Takes a long time currently (hacky)
    ##### homologene tests ####
    run_tests(method = "homologene")
})