longtests/testthat/test-validate_parameters.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

test_that("validate parameters", {
    ## 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)
    
        # Check that submitting incorrect parameters gives errors
        # Run MungeSumstats code
        # passing incorrect path
        not_file <- tempfile()
        error_return <-
            tryCatch(MungeSumstats::format_sumstats(not_file,
                ref_genome = "GRCh37",
                on_ref_genome = FALSE,
                strand_ambig_filter = FALSE,
                bi_allelic_filter = FALSE,
                allele_flip_check = FALSE,
                dbSNP=144
            ),
            error = function(e) e,
            warning = function(w) w
            )
        # incorrect ref genome
        error_return2 <-
            tryCatch(MungeSumstats::format_sumstats(file,
                ref_genome = "fake",
                on_ref_genome = FALSE,
                strand_ambig_filter = FALSE,
                bi_allelic_filter = FALSE,
                allele_flip_check = FALSE,
                dbSNP=144
            ),
            error = function(e) e,
            warning = function(w) w
            )
        # incorrect convert_small_p value
        error_return3 <-
            tryCatch(MungeSumstats::format_sumstats(file,
                ref_genome = "GRCh37",
                convert_small_p = "fake",
                on_ref_genome = FALSE,
                strand_ambig_filter = FALSE,
                bi_allelic_filter = FALSE,
                allele_flip_check = FALSE,
                dbSNP=144
            ),
            error = function(e) e,
            warning = function(w) w
            )
        # incorrect convert_n_int value
        error_return4 <-
            tryCatch(MungeSumstats::format_sumstats(file,
                ref_genome = "GRCh37",
                convert_n_int = "fake",
                on_ref_genome = FALSE,
                strand_ambig_filter = FALSE,
                bi_allelic_filter = FALSE,
                allele_flip_check = FALSE,
                dbSNP=144
            ),
            error = function(e) e,
            warning = function(w) w
            )
    
        # incorrect on_ref_genome value
        error_return5 <-
            tryCatch(MungeSumstats::format_sumstats(file,
                ref_genome = "GRCh37",
                on_ref_genome = "YES",
                strand_ambig_filter = FALSE,
                bi_allelic_filter = FALSE,
                allele_flip_check = FALSE,
                dbSNP=144
            ),
            error = function(e) e,
            warning = function(w) w
            )
    
        # incorrect strand_ambig_filter value
        error_return6 <-
            tryCatch(MungeSumstats::format_sumstats(file,
                ref_genome = "GRCh37",
                on_ref_genome = FALSE,
                strand_ambig_filter = "YES",
                bi_allelic_filter = FALSE,
                allele_flip_check = FALSE,
                dbSNP=144
            ),
            error = function(e) e,
            warning = function(w) w
            )
    
        # incorrect INFO_filter value
        error_return7 <-
            tryCatch(MungeSumstats::format_sumstats(file,
                ref_genome = "GRCh37",
                INFO_filter = TRUE,
                on_ref_genome = FALSE,
                strand_ambig_filter = FALSE,
                bi_allelic_filter = FALSE,
                allele_flip_check = FALSE,
                dbSNP=144
            ),
            error = function(e) e,
            warning = function(w) w
            )
    
        # incorrect N_std value
        error_return8 <-
            tryCatch(MungeSumstats::format_sumstats(file,
                ref_genome = "GRCh37",
                N_std = FALSE,
                on_ref_genome = FALSE,
                strand_ambig_filter = FALSE,
                bi_allelic_filter = FALSE,
                allele_flip_check = FALSE,
                dbSNP=144
            ),
            error = function(e) e,
            warning = function(w) w
            )
    
        # incorrect rmv_chr value
        error_return9 <-
            tryCatch(MungeSumstats::format_sumstats(file,
                ref_genome = "GRCh37",
                rmv_chr = c("X", "FAKE"),
                on_ref_genome = FALSE,
                strand_ambig_filter = FALSE,
                bi_allelic_filter = FALSE,
                allele_flip_check = FALSE,
                dbSNP=144
            ),
            error = function(e) e,
            warning = function(w) w
            )
    
        # incorrect bi_allelic value
        error_return10 <-
            tryCatch(MungeSumstats::format_sumstats(file,
                ref_genome = "GRCh37",
                on_ref_genome = FALSE,
                strand_ambig_filter = FALSE,
                bi_allelic_filter = "FAKE",
                allele_flip_check = FALSE,
                dbSNP=144
            ),
            error = function(e) e,
            warning = function(w) w
            )
    
        # incorrect allele_flip_check value
        error_return11 <-
            tryCatch(MungeSumstats::format_sumstats(file,
                ref_genome = "GRCh37",
                on_ref_genome = FALSE,
                strand_ambig_filter = FALSE,
                allele_flip_check = "FAKE",
                dbSNP=144
            ),
            error = function(e) e,
            warning = function(w) w
            )
    
        # Make sure ref_genome=NULL works
        ## Call uses reference genome as default with more than 2GB of memory,
        ## which is more than what 32-bit Windows can handle so
        # remove certain checks
        ## Removing for now, too time-intensive and is covered by other tests.
        # is_32bit_windows <-
        #     .Platform$OS.type == "windows" && .Platform$r_arch == "i386"
        # if (!is_32bit_windows) {
        #     pass_return1 <-
        #         tryCatch(MungeSumstats::format_sumstats(
        #             path = file,
        #             ref_genome = NULL
        #         ),
        #         error = function(e) e,
        #         warning = function(w) w
        #         )
        #     expect_true(file.exists(pass_return1))
        # }
    
    
        expect_true(is(error_return, "error"))
        expect_true(is(error_return2, "error"))
        expect_true(is(error_return3, "error"))
        expect_true(is(error_return4, "error"))
        expect_true(is(error_return5, "error"))
        expect_true(is(error_return6, "error"))
        expect_true(is(error_return7, "error"))
        expect_true(is(error_return8, "error"))
        expect_true(is(error_return9, "error"))
        expect_true(is(error_return10, "error"))
        expect_true(is(error_return11, "error"))
    }    
    else{
        expect_equal(is_32bit_windows, TRUE)
        expect_equal(is_32bit_windows, TRUE)
        expect_equal(is_32bit_windows, TRUE)
        expect_equal(is_32bit_windows, TRUE)
        expect_equal(is_32bit_windows, TRUE)
        expect_equal(is_32bit_windows, TRUE)
        expect_equal(is_32bit_windows, TRUE)
        expect_equal(is_32bit_windows, TRUE)
        expect_equal(is_32bit_windows, TRUE)
        expect_equal(is_32bit_windows, TRUE)
    }
})