longtests/testthat/test-on_ref_genome.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

test_that("SNPs not on reference genome are removed", {
  ## The following test uses more than 2GB of memory, which is more
  ## than what 32-bit Windows can handle:
  is_32bit_windows <- .Platform$OS.type == "windows" #&&
  #.Platform$r_arch == "i386"
  if (!is_32bit_windows) {
    file <- tempfile()
    # Update ID from line 3 to check it is deleted -
    # "rs79925071" is not on ref genome GRCh37
    eduAttainOkbay <- readLines(system.file("extdata", "eduAttainOkbay.txt",
                                            package = "MungeSumstats"
    ))
    eduAttainOkbay_missing <- eduAttainOkbay
    eduAttainOkbay_missing[3] <-
      "rs79925071\t6\t98584733\tA\tC\t0.5019\t0.024\t0.003\t2.457e-19"
    # 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 = TRUE,
                                                  strand_ambig_filter = FALSE,
                                                  bi_allelic_filter = FALSE,
                                                  allele_flip_check = FALSE,
                                                  log_folder_ind = TRUE,
                                                  infer_eff_direction = FALSE,
                                                  dbSNP=144
    )
    reformatted_lines <- data.table::fread(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,#TRUE, for speed
                                          strand_ambig_filter = FALSE,
                                          bi_allelic_filter = FALSE,
                                          allele_flip_check = FALSE,
                                          infer_eff_direction = FALSE,
                                          dbSNP=144
    )
    org_lines <- data.table::fread(org)
    #test
    expect_equal(all.equal(reformatted_lines, org_lines), TRUE)
    # also check get genome builds works
    eduAttainOkbayPth <- system.file("extdata", "eduAttainOkbay.txt",
                                     package = "MungeSumstats"
    )
    sumstats_list <- list(ss1 = eduAttainOkbayPth)
    ref_genomes <- get_genome_builds(
      sumstats_list = sumstats_list,
      sampled_snps = 19,
      dbSNP = 144,
      chr_filt = c("1","2","3","4") #filtering to reduce computational burden
    )
    expect_equal(all.equal(ref_genomes, list("ss1" = "GRCH37")), TRUE)
  } else {
    expect_equal((is_32bit_windows||!Sys.info()["sysname"]=="Linux"), TRUE)
    expect_equal((is_32bit_windows||!Sys.info()["sysname"]=="Linux"), TRUE)
  }
})