longtests/testthat/test-no_chr_bp.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

test_that("Imputation of CHR and BP correctly", {
    ## The following test uses more than 2GB of memory, which is more
    ## than what 32-bit Windows can handle:
    is_32bit_windows <- .Platform$OS.type == "windows" ##&&
        ##.Platform$r_arch == "i386"
    if (!is_32bit_windows) {
        file <- tempfile()
        # write the Educational Attainment GWAS to a temp file for testing
        eduAttainOkbay <- readLines(system.file("extdata", "eduAttainOkbay.txt",
                                                package = "MungeSumstats"
        ))
        writeLines(eduAttainOkbay, con = file)
        # read it in and drop CHR BP columns
        sumstats_dt <- data.table::fread(file)
        # Keep Org to validate values
        sumstats_dt_missing <- data.table::copy(sumstats_dt)
        sumstats_dt_missing[, CHR := NULL]
        sumstats_dt_missing[, POS := NULL]
        data.table::fwrite(x = sumstats_dt_missing, file = file, sep = "\t")
        # Run MungeSumstats code
        reformatted <- MungeSumstats::format_sumstats(file,
            ref_genome = "GRCh37",
            on_ref_genome = FALSE,
            strand_ambig_filter = FALSE,
            bi_allelic_filter = FALSE,
            allele_flip_check = FALSE,
            log_folder_ind = TRUE,
            dbSNP=144
        )
        res_dt <- data.table::fread(reformatted$sumstats)
        # correct names of MungeSumstats::eduAttainOkbay
        names(sumstats_dt) <- c(
            "SNP", "CHR", "BP", "A1", "A2",
            "FRQ", "Beta", "SE", "P"
        )
        # get order same
        setkey(res_dt, SNP)
        setkey(sumstats_dt, SNP)
        # add CHR, BP to org
        sumstats_dt[res_dt, CHR_der := i.CHR]
        sumstats_dt[res_dt, BP_der := i.BP]
        # remove any that weren't found in reference
        sumstats_dt <- sumstats_dt[complete.cases(sumstats_dt), ]
        expect_equal(sumstats_dt$BP, sumstats_dt$BP_der)
        expect_equal(sumstats_dt$CHR, sumstats_dt$CHR_der)
    } else {
        expect_equal(is_32bit_windows, TRUE)
        expect_equal(is_32bit_windows, TRUE)
    }
})