longtests/testthat/test-rs_plus.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

test_that("Handle extra info in rs id column", {
    ## 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()
        # create dataset to test
        set.seed(101)
        a <- data.table::data.table(
            SNP = c(
                "rs140052487:C:A", "rs558796213:G:T",
                "rs561234294:A:G", "rs2462492:C:T",
                "rs548455890:T:G"
            ),
            "P" = (runif(5) / 10),
            "FRQ" = runif(5), "BETA" = runif(5), "CHR" = rep(1, 5),
            "BP" = c(54353, 54564, 54591, 54676, 54763)
        )
        # Run MungeSumstats code
        reformatted <- MungeSumstats::format_sumstats(a,
            ref_genome = "GRCh37",
            on_ref_genome = FALSE,
            strand_ambig_filter = FALSE,
            bi_allelic_filter = FALSE,
            allele_flip_check = FALSE,
            log_folder_ind = TRUE,
            imputation_ind = FALSE,
            return_data = TRUE,
            dbSNP=144
        )
    
        # Should equal separated version
        set.seed(101)
        b <- data.table::data.table(
            SNP = c(
                "rs140052487", "rs558796213", "rs561234294",
                "rs2462492", "rs548455890"
            ), "P" = (runif(5) / 10),
            "FRQ" = runif(5), "BETA" = runif(5), "CHR" = rep(1, 5),
            "BP" = c(54353, 54564, 54591, 54676, 54763),
            "A1" = c("C", "G", "A", "C", "T"), "A2" = c("A", "T", "G", "T", "G")
        )
        reformatted2 <- MungeSumstats::format_sumstats(b,
            ref_genome = "GRCh37",
            on_ref_genome = FALSE,
            strand_ambig_filter = FALSE,
            bi_allelic_filter = FALSE,
            allele_flip_check = FALSE,
            log_folder_ind = TRUE,
            imputation_ind = TRUE,
            return_data = TRUE,
            dbSNP=144
        )
        # should be the same
        expect_equal(setequal(reformatted$sumstats, reformatted2$sumstats), TRUE)
    }    
    else{
        expect_equal(is_32bit_windows, TRUE)
    }
})