longtests/testthat/test-multi_traits.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

test_that("Multi-trait GWAS handled correctly", {
    ## Call uses reference genome as default with more than 2GB of memory,
    ## which is more than what 32-bit Windows can handle so remove tests
    is_32bit_windows <-
        .Platform$OS.type == "windows" && .Platform$r_arch == "i386"
    if (!is_32bit_windows) {
        file <- tempfile()
        # write an example of a multi-trait GWAS in
        multi_trait <- c(
            "chromosome\trs_id\tmarkername\tposition_hg18\tEffect_allele\tOther_allele\tEAF_HapMapCEU\tN_SMK\tEffect_SMK\tStdErr_SMK\tP_value_SMK\tN_NONSMK\tEffect_NonSMK\tStdErr_NonSMK\tP_value_NonSMK",
            "1\t\tchr1:240307304\t240307304\tT\tG\t\t31366.8\t-0.0528\t0.0142\t0.0002004\t121792\t-0.0026\t0.0075\t0.7274",
            "1\trs1000050\tchr1:161003087\t161003087\tT\tC\t0.9\t36256.6\t0.0001\t0.0109\t0.9931\t127514\t0.0058\t0.0059\t0.3307",
            "1\trs1000073\tchr1:155522020\t155522020\tA\tG\t0.3136\t36335\t0.0046\t0.0083\t0.5812\t126780\t0.0038\t0.0045\t0.3979",
            "1\trs1000075\tchr1:94939420\t94939420\tT\tC\t0.3583\t38959.3\t-0.0013\t0.0082\t0.8687\t147567\t-0.0043\t0.0044\t0.3259",
            "1\trs1000085\tchr1:66630503\t66630503\tC\tG\t0.1667\t38761\t0.0053\t0.0095\t0.5746\t147259\t-0.0034\t0.0052\t0.5157"
        )
        writeLines(multi_trait, con = file)
        # Run MungeSumstats code
        reformatted <- MungeSumstats::format_sumstats(file,
            ref_genome = "GRCh37",
            analysis_trait = "smk",
            on_ref_genome = FALSE,
            strand_ambig_filter = FALSE,
            bi_allelic_filter = FALSE,
            allele_flip_check = FALSE,
            sort_coordinates = FALSE,
            chr_style = "UCSC",
            dbSNP=144
        )
        reformatted_res <- readLines(reformatted)
        # check manually
        multi_trait_res_smk <- c(
            "SNP\tCHR\tBP\tA1\tA2\tPOSITION_HG18\tEAF_HAPMAPCEU\tN\tBETA\tSE\tP\tN_NONSMK\tEFFECT_NONSMK\tSTDERR_NONSMK\tP_VALUE_NONSMK",
            "rs1000073\tchr1\t155522020\tG\tA\t155522020\t0.3136\t36335\t0.0046\t0.0083\t0.5812\t126780\t0.0038\t0.0045\t0.3979",
            "rs1000050\tchr1\t161003087\tC\tT\t161003087\t0.9\t36257\t1e-04\t0.0109\t0.9931\t127514\t0.0058\t0.0059\t0.3307",
            "rs1000085\tchr1\t66630503\tG\tC\t66630503\t0.1667\t38761\t0.0053\t0.0095\t0.5746\t147259\t-0.0034\t0.0052\t0.5157",
            "rs1000075\tchr1\t94939420\tC\tT\t94939420\t0.3583\t38959\t-0.0013\t0.0082\t0.8687\t147567\t-0.0043\t0.0044\t0.3259"
        )
        expect_equal(setequal(multi_trait_res_smk, reformatted_res), TRUE)
    }
    else{
        expect_equal(is_32bit_windows, TRUE)
    }
})