longtests/testthat/test-bi_alllelic.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

test_that("non-biallelic SNPs are removed", {
    ## 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()
        # Update ID from line 3 to check it is deleted -
        # rs9320913 is non-biallelic
        problem_snp <- "rs9320913"
        eduAttainOkbay <- readLines(system.file("extdata", "eduAttainOkbay.txt",
                                                package = "MungeSumstats"
        ))
        eduAttainOkbay_missing <- eduAttainOkbay
        eduAttainOkbay_missing[3] <-
            "rs1871109\t6\t98584733\tA\tC\t0.5019\t0.024\t0.003\t2.457e-19"
        
        # write the Educational Attainment GWAS to a temp file for testing
        writeLines(eduAttainOkbay_missing, con = file)
        # Run MungeSumstats code
        reformatted <- MungeSumstats::format_sumstats(file,
            ref_genome = "GRCh37",
            on_ref_genome = FALSE,
            strand_ambig_filter = FALSE,
            bi_allelic_filter = TRUE,
            allele_flip_check = FALSE,
            log_folder_ind = TRUE,
            dbSNP=144
        )
        reformatted_lines <- readLines(reformatted$sumstats)
        # Should equal org apart from this one line
        writeLines(eduAttainOkbay, con = file)
        org <- MungeSumstats::format_sumstats(file,
            ref_genome = "GRCh37",
            on_ref_genome = FALSE,
            strand_ambig_filter = FALSE,
            bi_allelic_filter = TRUE,
            allele_flip_check = FALSE,
            dbSNP=144
        )
        org_lines <- readLines(org)

        rsid_index <- grep(problem_snp, org_lines, ignore.case = TRUE)
        # reordering in function, line 3 rs9320913 is now 58
        testthat::expect_equal(
            setequal(reformatted_lines, org_lines[-rsid_index]),
            TRUE
        )
    } else {
        testthat::expect_equal(is_32bit_windows, TRUE)
    }
})