longtests/testthat/test-n_num.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

test_that("Handle n when its 5 std dev > mean", {
    ## 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 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 make N
    sumstats_dt <- data.table::fread(file)
    # Add N column and make it not an integer
    sumstats_dt[, N := round(10 * runif(nrow(sumstats_dt)), 0)]
    # Ensure 1 value is > 5std dev above the mean
    # Remember creating and adding in this value will increase the mean and sd
    mean_N <- mean(sumstats_dt$N)
    sd_N <- stats::sd(sumstats_dt$N)
    bigger_value <- mean_N + (6 * sd_N)
    data.table::set(sumstats_dt, i = 1L, j = "N", value = bigger_value)
    data.table::fwrite(x = sumstats_dt, file = file, sep = "\t")
    # ensure this SNP is removed
    rmv_snp <- sumstats_dt$MarkerName[1]
    # Run MungeSumstats code
    # Don't convert n to integers as this may round down
    reformatted <- MungeSumstats::format_sumstats(file,
        ref_genome = "GRCh37",
        N_std = 5, convert_n_int = FALSE,
        on_ref_genome = FALSE,
        strand_ambig_filter = FALSE,
        bi_allelic_filter = FALSE,
        allele_flip_check = FALSE,
        log_folder_ind = TRUE,
        dbSNP=144
    )
    res_dt <- data.table::fread(reformatted$sumstats)
    expect_equal(!(rmv_snp %in% res_dt$SNP), TRUE)

    # Run MungeSumstats code
    # Don't convert n to integers as this may round down
    # set N_dropNA to TRUE
    reformatted <- MungeSumstats::format_sumstats(file,
        ref_genome = "GRCh37",
        N_std = 5, convert_n_int = FALSE,
        on_ref_genome = FALSE,
        strand_ambig_filter = FALSE,
        bi_allelic_filter = FALSE,
        allele_flip_check = FALSE,
        log_folder_ind = TRUE,
        N_dropNA = TRUE,
        dbSNP=144
    )
    res_dt <- data.table::fread(reformatted$sumstats)

    # set N_dropNA to FALSE
    reformatted2 <- MungeSumstats::format_sumstats(file,
        ref_genome = "GRCh37",
        N_std = 5, convert_n_int = FALSE,
        on_ref_genome = FALSE,
        strand_ambig_filter = FALSE,
        bi_allelic_filter = FALSE,
        allele_flip_check = FALSE,
        log_folder_ind = TRUE,
        N_dropNA = FALSE,
        dbSNP=144
    )
    res_dt2 <- data.table::fread(reformatted2$sumstats)
    expect_equal(!(rmv_snp %in% res_dt$SNP), TRUE)
    # should be no na's
    expect_equal(all.equal(res_dt, res_dt2), TRUE)
    }    
    else{
        expect_equal(is_32bit_windows, TRUE)
        expect_equal(is_32bit_windows, TRUE)
    }
})