tests/testthat/test-calculate_conditional_geneset_enrichment.R

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

test_that("calculate_conditional_geneset_enrichment works", {
     
    if(!is_32bit()){
        ctd <- MAGMA.Celltyping::get_ctd("ctd_allKI")
        magma_dir <- MAGMA.Celltyping::import_magma_files(ids = "ieu-a-298")
        geneset <- MAGMA.Celltyping::rbfox_binding

        res <-  calculate_conditional_geneset_enrichment(
            geneset = geneset,
            ctd = ctd,
            controlledAnnotLevel = 1,
            controlledCTs = "pyramidal SS",
            magma_dir = magma_dir,
            analysis_name = "Rbfox_16_pyrSS",
            geneset_species = "mouse",
            ctd_species = "mouse")
        testthat::expect_true(methods::is(res,"data.frame"))
        cols <- c("NGENES","BASELINE_BETA","BASELINE_BETA_STD",
                  "BASELINE_SE","BASELINE_P",
                  "COND_BETA","COND_BETA_STD","COND_SE",
                  "COND_P","conditionedCTs",
                  "z","p_twoSided","p_oneSided")
        testthat::expect_true(all(cols %in% colnames(res)))
    } else {
        testthat::expect_null(NULL)
    }
})