tests/testthat/test-prepare_files.R

In RGLab/HIPCMatrix: Microarray and RNA-seq Processing for ImmuneSpace

.prep_geo_files <- HIPCMatrix:::.prep_geo_files

test_that("select_input_files selects the correct files", {
  supp_files_dir <- "test_data/sdy787/supp_files/T-cell_ARM3144"
  expect_equal(
    HIPCMatrix:::.select_input_files(supp_files_dir),
    file.path(supp_files_dir, "GSE113891_PT_all_Count.tsv")
  )
})

test_that("immport files are loaded correctly", {
  verbose <- TRUE
  # SDY1630: RNA-seq
  study <- "SDY1630"
  gef <- readRDS("test_data/sdy1630/SDY1630_gef.rds")
  platform <- "NA"
  input_files <- "GSE133383_filtered_NKcounts_table.748979.csv"
  analysis_dir <- "test_data/sdy1630"
  files <- HIPCMatrix:::.prep_immport_files(
    study,
    gef,
    platform,
    file.path(analysis_dir, input_files),
    analysis_dir,
    verbose
  )
  expect_equal(files, "test_data/sdy1630/supp_files/Spleen_ARM5244/SDY1630_raw_expression.txt")

  # SDY112: Affy
  study <- "SDY112"
  gef <- readRDS("test_data/sdy112/SDY112_gef.rds")
  analysis_dir <- "test_data/sdy112"
  platform <- "Affymetrix"
  input_files <- HIPCMatrix:::.select_input_files(analysis_dir)

  # Should do nothing
  files <- HIPCMatrix:::.prep_immport_files(
    study,
    gef,
    platform,
    input_files,
    analysis_dir,
    verbose
  )
  expect_true(all(input_files == files))

  # should error when one of the files is not CEL file
  input_files <- list.files(analysis_dir)
  expect_error(
    files <- HIPCMatrix:::.prep_immport_files(
      study,
      gef,
      platform,
      input_files,
      analysis_dir,
      verbose
    ),
    "Affymetrix should only have CEL input files"
  )

  # SDY645: Illumina
  study <- "SDY387"
  input_files <- "SDY387_EXP13732_microarray.703288.tsv"
  gef <- readRDS("test_data/sdy387/SDY387_gef.rds")
  analysis_dir <- "test_data/sdy387"
  platform <- "Illumina"
  input_files <- unique(gef$file_info_name)
  files <- HIPCMatrix:::.prep_immport_files(
    study,
    gef,
    platform,
    file.path(analysis_dir, input_files),
    analysis_dir,
    verbose = FALSE
  )
  expect_equal(
    files,
    "test_data/sdy387/supp_files/Whole-blood_ARM2325/SDY387_raw_expression.txt"
  )
})

test_that(".prep_geo_files GSM SOFT", {
  meta_data <- list(
    file_location = "gsm_soft",
    platform = "Illumina",
    gsm_table_var_name = "AVERAGE_SIGNAL"
  )
  gef <- con_all$getDataset("gene_expression_files",
    colFilter = Rlabkey:::makeFilter(c("biosample_accession", "IN", "BS974298")),
    original_view = TRUE
  )
  analysis_dir <- "test_data/sdy1289"
  expect_log_message(
    input_files <- .prep_geo_files("SDY1289",
      gef,
      meta_data,
      input_files = NA,
      analysis_dir,
      verbose = TRUE,
      reload = FALSE
    ),
    "Downloading GSM soft files to test_data/sdy1289/supp_files/Whole-blood_ARM4455"
  )
  expect_equal(input_files, "test_data/sdy1289/supp_files/Whole-blood_ARM4455/SDY1289_raw_expression.txt")
})
test_that(".prep_geo_files GSM supp illumina", {
  meta_data <- get_meta_data("SDY180",
    baseUrl = labkey.url.base
  )
  gef <- con_all$getDataset("gene_expression_files",
    colFilter = Rlabkey:::makeFilter(c("biosample_accession", "IN", "BS662409;BS662402")),
    original_view = TRUE
  )[!is.na(geo_accession)]
  analysis_dir <- "test_data/sdy180"
  expect_log_message(
    input_files <- .prep_geo_files("SDY180",
      gef,
      meta_data,
      input_files = NA,
      analysis_dir,
      verbose = TRUE,
      reload = FALSE
    ),
    "Downloading GSM supp files to test_data/sdy180/supp_files/Whole-blood_ARM773"
  )
  expect_equal(input_files, "test_data/sdy180/supp_files/Whole-blood_ARM773/SDY180_raw_expression.txt")
})
test_that(".prep_geo_files GSM supp affy", {
  meta_data <- get_meta_data("SDY1328",
    baseUrl = labkey.url.base
  )
  gef <- con_all$getDataset("gene_expression_files",
    colFilter = Rlabkey:::makeFilter(c("biosample_accession", "IN", "BS1005477;BS978363;BS1005596")),
    original_view = TRUE
  )[!is.na(geo_accession)]
  analysis_dir <- "test_data/sdy1328"
  expect_log_message(
    input_files <- .prep_geo_files("SDY1328",
      gef,
      meta_data,
      input_files = NA,
      analysis_dir,
      verbose = TRUE,
      reload = FALSE
    ),
    "Downloading GSM supp files to test_data/sdy1328/supp_files/Whole-blood_ARM4537"
  )
  # Expect two GSM for BS1005477
  expect_length(input_files, 4)
  expect_true(all(grepl("CEL", input_files)))
})
test_that(".prep_geo_files GSM supp rnaseq", {
  meta_data <- list(
    file_location = "gsm_supp_files",
    platform = "NA"
  )
  gef <- con_all$getDataset("gene_expression_files",
    colFilter = Rlabkey:::makeFilter(c("biosample_accession", "IN", "BS1004262;BS1004309")),
    original_view = TRUE
  )[!is.na(geo_accession)]
  analysis_dir <- "test_data/sdy1412"
  expect_log_message(
    input_files <- .prep_geo_files("SDY1412",
      gef,
      meta_data,
      input_files = NA,
      analysis_dir,
      verbose = TRUE,
      reload = FALSE
    ),
    "GSM3494630"
  )
  expect_true(grepl("SDY1412_raw_expression.txt", input_files))
  ge <- fread(input_files)
  expect_equal(ncol(ge), 3)
})


test_that(".prep_geo_files GSE supp illumina", {
  meta_data <- get_meta_data("SDY640",
    baseUrl = labkey.url.base
  )
  gef <- con_all$getDataset("gene_expression_files",
    colFilter = Rlabkey:::makeFilter(c("biosample_accession", "IN", "BS799828")),
    original_view = TRUE
  )[!is.na(geo_accession)]
  analysis_dir <- "test_data/sdy640"
  expect_log_message(
    input_files <- .prep_geo_files("SDY640",
      gef,
      meta_data,
      input_files = NA,
      analysis_dir,
      verbose = TRUE,
      reload = FALSE
    ),
    "Using saved supp files for GSE101710"
  )
  expect_true(grepl("SDY640_raw_expression.txt", input_files))
})

test_that(".prep_geo_files GSE supp rnaseq", {
  meta_data <- get_meta_data("SDY787",
    baseUrl = labkey.url.base
  )
  gef <- readRDS("test_data/sdy787/SDY787_gef.rds")[1, ]
  analysis_dir <- "test_data/sdy787"
  # Message from GEOquery
  expect_message(
    input_files <- HIPCMatrix:::.prep_geo_files("SDY787",
      gef,
      meta_data,
      input_files = NA,
      analysis_dir,
      verbose = TRUE,
      reload = FALSE
    ),
    "Using locally cached version of GSM3122900"
  )
  expect_equal(input_files, "test_data/sdy787/supp_files/T-cell_ARM3144/SDY787_raw_expression.txt")
})