longtests/testthat/test-check_tabular.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

test_that("Check that a file is in tabular format", {
    ## 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) {
        ### read data
        path <- 
            system.file("extdata", "eduAttainOkbay.txt", 
                            package = "MungeSumstats")
        sumstats_dt <- data.table::fread(path, nThread = 1)
        ### Test tsv
        header <- read_header(path = path)
        is_tabular_tsv <- check_tabular(header = header)
        ### Test csv
        path_csv <- tempfile()
        data.table::fwrite(sumstats_dt, path_csv, sep = ",")
        header <- read_header(path = path_csv)
        is_tabular_csv <- check_tabular(header = header)
        #### Test space-separated
        path_space <- tempfile()
        data.table::fwrite(sumstats_dt, path_space, sep = " ")
        header <- read_header(path = path_space)
        is_tabular_space <- check_tabular(header = header)
        expect_equal(all.equal(is_tabular_tsv, is_tabular_csv, 
                                is_tabular_space), TRUE)
    }    
    else{
        expect_equal(TRUE, TRUE)
    }
})