tests/testthat/test-calculate_conditional_celltype_enrichment_limma.R

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

test_that("calculate_conditional_celltype_enrichment_limma works", {
    
    ## Encompasses tests for:
    ## - calculate_conditional_celltype_enrichment_limma
    ## - adjust_zstat_in_genesOut
    ## - calculate_celltype_enrichment_limma
    ## ...since calculate_conditional_celltype_enrichment_limma
    ## uses the latter two.
    
    if(!is_32bit()){
        ctd <- ewceData::ctd()
        magma_cols <- c("entrez","hgnc_symbol",
                        "CHR","START","STOP","NSNPS","NPARAM",
                        "N","ZSTAT","P","hgnc_symbol","Q","logNSNPS","logNPARAM",
                        "GENELEN","logGENELEN","ADJ_ZSTAT")
        
        #### MAGMA 1 #####
        genesOut1 <- MAGMA.Celltyping::import_magma_files(
            ids = c("ieu-a-298"),
            file_types = ".genes.out",
            return_dir = FALSE)
        magma1 <- MAGMA.Celltyping::adjust_zstat_in_genesOut(
            ctd = ctd,
            magma_GenesOut_file = genesOut1)
        testthat::expect_true(file.exists(genesOut1))
        testthat::expect_true(all(magma_cols %in% colnames(magma1)))
        
        #### MAGMA 2 #####
        genesOut2 <- MAGMA.Celltyping::import_magma_files(
            ids = c("ukb-a-333"),
            file_types = ".genes.out",
            return_dir = FALSE)
        magma2 <- MAGMA.Celltyping::adjust_zstat_in_genesOut(
            ctd = ctd,
            magma_GenesOut_file = genesOut2)
        testthat::expect_true(file.exists(genesOut2))
        testthat::expect_true(all(magma_cols %in% colnames(magma2)))
        
        #### Run conditional enrichment ####
        annotLevel <- 1
        cond_res <- MAGMA.Celltyping::calculate_conditional_celltype_enrichment_limma(
            magma1 = magma1,
            magma2 = magma2,
            annotLevel = annotLevel,
            ctd = ctd)
        
        testthat::expect_true(
            all(c("Celltype","ps","coef","p1_baseline","p2_baseline","qs") %in% 
                    colnames(cond_res)))
        celltypes <- EWCE::fix_celltype_names(
            celltypes = colnames(ctd[[annotLevel]]$specificity))
        testthat::expect_equal(sort(cond_res$Celltype), sort(celltypes))
    } else {
        testthat::expect_null(NULL)
    }
})