longtests/testthat/test-check_imputation_cols.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

test_that("Check that imputation columns added correctly", {
  ## 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) {
    pth <- system.file("extdata", "eduAttainOkbay.txt",
                       package = "MungeSumstats"
    )
    #only run not on linux to speed up linux bioc checks
    eduAttainOkbay <- data.table::fread(pth)
    # edit to make an rs id be imputed
    eduAttainOkbay[1, "MarkerName"] <-
      substring(
        eduAttainOkbay[1, "MarkerName"], 3,
        nchar(eduAttainOkbay[1, "MarkerName"])
      )
    # write to temp dir
    file <- tempfile()
    data.table::fwrite(eduAttainOkbay, file)
    # run
    reformatted <- MungeSumstats::format_sumstats(file,
                                                  ref_genome = "GRCh37",
                                                  compute_z = TRUE,
                                                  compute_n = 1001,
                                                  save_format='LDSC',
                                                  imputation_ind = TRUE,
                                                  allele_flip_check = TRUE,
                                                  dbSNP=144
    )
    res <- data.table::fread(reformatted)
    col_headers <- names(res)
    imputat_cols <- c(
      col_headers[grepl("^IMPUTATION_", col_headers)],
      "flipped"["flipped" %in% col_headers],
      col_headers[grepl("^convert_", col_headers)]
    )
    # just check imputation columns exist
    expect_equal(length(imputat_cols) > 0, TRUE)
    # also check all have at least 1 value present
    have_value <- TRUE
    for (col_i in imputat_cols) {
      col_i_val <- res[[col_i]]
      if (length(col_i_val[!is.na(col_i_val)]) == 0) {
        have_value <- FALSE
      }
    }
    expect_equal(have_value, TRUE)
    # check other compute_n values
    eduAttainOkbay <- data.table::fread(pth)
    eduAttainOkbay[, N_CON := 100]
    eduAttainOkbay[, N_CAS := 120]
    # write to temp dir
    file <- tempfile()
    data.table::fwrite(eduAttainOkbay, file)
    methods <- c("ldsc", "sum", "giant", "metal")
    reformatted <- MungeSumstats::format_sumstats(file,
                                                  ref_genome = "GRCh37",
                                                  compute_n = methods,
                                                  on_ref_genome = FALSE,
                                                  strand_ambig_filter = FALSE,
                                                  bi_allelic_filter = FALSE,
                                                  allele_flip_check = FALSE,
                                                  dbSNP=144
    )
    res <- data.table::fread(reformatted)
    expect_equal(all(paste0("Neff_", c("ldsc", "giant", "metal")) %in%
                       colnames(res)), TRUE)
  } else {
    expect_equal(is_32bit_windows, TRUE)
    expect_equal(is_32bit_windows, TRUE)
    expect_equal(is_32bit_windows, TRUE)
  }
})