longtests/testthat/test-user_mapping_file.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

test_that("Test that user inputted mapping file is appropriate", {
    ## 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()
        eduAttainOkbay <- readLines(system.file("extdata", "eduAttainOkbay.txt",
            package = "MungeSumstats"
        ))
        # write the Educational Attainment GWAS to a temp file for testing
        writeLines(eduAttainOkbay, con = file)
    
        # define mapping file - leave out some essential columns - A2
        data("sumstatsColHeaders")
        essential_cols <- c("SNP", "CHR", "BP", "P", "A1", "A2")
        signed_cols <- c("Z", "OR", "BETA", "LOG_ODDS", "SIGNED_SUMSTAT")
        user_map <- sumstatsColHeaders[sumstatsColHeaders$Corrected %in%
            essential_cols[-6] |
            sumstatsColHeaders$Corrected %in%
                signed_cols, ]
        # Run MungeSumstats code
        fail_return <-
            tryCatch(MungeSumstats::format_sumstats(file,
                ref_genome = "GRCh37",
                mapping_file = user_map
            ),
            error = function(e) e,
            warning = function(w) w
            )
        catch <- is(fail_return, "error")||
          !is.character(fail_return)||!file.exists(fail_return)
        expect_equal(catch, TRUE)
        # update user map to contain all essential columns
        user_map2 <- sumstatsColHeaders[sumstatsColHeaders$Corrected %in%
            essential_cols |
            sumstatsColHeaders$Corrected %in%
                signed_cols, ]
        # This time should run
        reformatted <- MungeSumstats::format_sumstats(file,
            ref_genome = "GRCh37",
            on_ref_genome = FALSE,
            strand_ambig_filter = FALSE,
            bi_allelic_filter = FALSE,
            allele_flip_check = FALSE,
            mapping_file = user_map2,
            return_data = TRUE,
            return_format = "GRanges",
            dbSNP=144
        )
    
    
        expect_equal(is(reformatted, "GRanges"), TRUE)
    }    
    else{
        expect_equal(is_32bit_windows, TRUE)
    }
})