longtests/testthat/test-on_x_y_mt_chr.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

test_that("SNPs on X,Y,MT chromosome are removed", {
    ## 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()
        # Update CHR from line 3,4,5 to X,Y,MT to check it is deleted -
        eduAttainOkbay <- readLines(system.file("extdata", "eduAttainOkbay.txt",
            package = "MungeSumstats"
        ))
        eduAttainOkbay_missing <- eduAttainOkbay
        eduAttainOkbay_missing[3] <-
            "rs9320913\tX\t98584733\tA\tC\t0.5019\t0.024\t0.003\t2.457e-19"
        eduAttainOkbay_missing[4] <-
            "rs11712056\tY\t49914397\tT\tC\t0.5504\t0.024\t0.003\t3.304e-19"
        eduAttainOkbay_missing[5] <-
            "rs148734725\tMT\t49406708\tA\tG\t0.3078\t0.025\t0.003\t1.363e-18"
    
        problem_snp <- c("rs9320913", "rs11712056", "rs148734725")
        # 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 = FALSE,
            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 = FALSE,
            allele_flip_check = FALSE,
            dbSNP=144
        )
        org_lines <- readLines(org)
        rsid_index <- grep(paste(problem_snp, collapse = "|"), org_lines,
            ignore.case = TRUE
        )
        # reordering in function, line 3,4,5 is now 28,58
        expect_equal(setequal(
            reformatted_lines,
            org_lines[-rsid_index]
        ), TRUE)
    }    
    else{
        expect_equal(is_32bit_windows, TRUE)
    }
})