tests/testthat/test-msms-search-lipidmaps.R

In ricoderks/Rcpm: General functions for the Center of Proteomics and Metabolomics (LUMC)

# define an input stuff according to the help documentation for the tests!

mypeaks <- c("818.59 10000 1\n758.57 20\n687.50 20\n506.33 50\n494.33 15\n488.31 2")

# test the input
context("msms-search-lipidmaps: input check")

test_that("Is input correct:", {
  expect_error(msms_search_lipidmaps(lipidclass = "phoslipids",
                                     intensity_threshold = 10,
                                     prec_tol = 0.01,
                                     prod_tol = 0.01,
                                     headgroup = "Any",
                                     ion = "formate",
                                     min_matches = 2,
                                     LIMIT = "All",
                                     peaklist = mypeaks),
               "'arg' should be one of \"glycerolipids\", \"phospholipids\"")
  expect_error(msms_search_lipidmaps(lipidclass = "phospholipids",
                                     intensity_threshold = 10,
                                     prec_tol = 0.01,
                                     prod_tol = 0.01,
                                     headgroup = "Any",
                                     ion = "formate",
                                     min_matches = 2,
                                     LIMIT = "All"),
               "No 'peaklist' given!")
  expect_error(msms_search_lipidmaps(lipidclass = "phospholipids",
                                     intensity_threshold = 10,
                                     prec_tol = 0.01,
                                     prod_tol = 0.01,
                                     headgroup = "TG",
                                     ion = "formate",
                                     min_matches = 2,
                                     LIMIT = "All",
                                     peaklist = mypeaks),
               "'arg' should be one of \"Any\", \"PC\", \"PA\", \"PS\", \"PE\", \"PG\", \"PI\"")
  expect_error(msms_search_lipidmaps(lipidclass = "glycerolipids",
                                     intensity_threshold = 10,
                                     prec_tol = 0.01,
                                     prod_tol = 0.01,
                                     headgroup = "PC",
                                     ion = "ammonium",
                                     min_matches = 2,
                                     LIMIT = "All",
                                     peaklist = mypeaks),
               "'arg' should be one of \"All\", \"MG\", \"DG\", \"TG\"")
  expect_error(msms_search_lipidmaps(lipidclass = "glycerolipids",
                                     intensity_threshold = 10,
                                     prec_tol = 0.01,
                                     prod_tol = 0.01,
                                     headgroup = "Any",
                                     ion = "fornate",
                                     min_matches = 2,
                                     LIMIT = "All",
                                     peaklist = mypeaks),
               "'arg' should be one of \"ammonium\"")
  expect_error(msms_search_lipidmaps(lipidclass = "phospholipids",
                                     intensity_threshold = 10,
                                     prec_tol = 0.01,
                                     prod_tol = 0.01,
                                     headgroup = "Any",
                                     ion = "ammonium",
                                     min_matches = 2,
                                     LIMIT = "All",
                                     peaklist = mypeaks),
               "'arg' should be one of \"chloride\", \"acetate\", \"formate\"")
  expect_error(msms_search_lipidmaps(lipidclass = "phospholipids",
                                     intensity_threshold = -10,
                                     prec_tol = 0.01,
                                     prod_tol = 0.01,
                                     headgroup = "Any",
                                     ion = "formate",
                                     min_matches = 2,
                                     LIMIT = "All",
                                     peaklist = mypeaks),
               "'intensity_threshold' should be possitive!")
  expect_error(msms_search_lipidmaps(lipidclass = "phospholipids",
                                     intensity_threshold = "10",
                                     prec_tol = 0.01,
                                     prod_tol = 0.01,
                                     headgroup = "Any",
                                     ion = "formate",
                                     min_matches = 2,
                                     LIMIT = "All",
                                     peaklist = mypeaks),
               "'intensity_threshold' needs to be a number!")
  expect_error(msms_search_lipidmaps(lipidclass = "phospholipids",
                                     intensity_threshold = 10,
                                     prec_tol = -0.01,
                                     prod_tol = 0.01,
                                     headgroup = "Any",
                                     ion = "formate",
                                     min_matches = 2,
                                     LIMIT = "All",
                                     peaklist = mypeaks),
               "'prec_tol' should be possitive!")
  expect_error(msms_search_lipidmaps(lipidclass = "phospholipids",
                                     intensity_threshold = 10,
                                     prec_tol = "0.01",
                                     prod_tol = 0.01,
                                     headgroup = "Any",
                                     ion = "formate",
                                     min_matches = 2,
                                     LIMIT = "All",
                                     peaklist = mypeaks),
               "'prec_tol' needs to be a number!")
  expect_error(msms_search_lipidmaps(lipidclass = "phospholipids",
                                     intensity_threshold = 10,
                                     prec_tol = 0.01,
                                     prod_tol = -0.01,
                                     headgroup = "Any",
                                     ion = "formate",
                                     min_matches = 2,
                                     LIMIT = "All",
                                     peaklist = mypeaks),
               "'prod_tol' should be possitive!")
  expect_error(msms_search_lipidmaps(lipidclass = "phospholipids",
                                     intensity_threshold = 10,
                                     prec_tol = 0.01,
                                     prod_tol = "0.01",
                                     headgroup = "Any",
                                     ion = "formate",
                                     min_matches = 2,
                                     LIMIT = "All",
                                     peaklist = mypeaks),
               "'prod_tol' needs to be a number!")
  expect_error(msms_search_lipidmaps(lipidclass = "phospholipids",
                                     intensity_threshold = 10,
                                     prec_tol = 0.01,
                                     prod_tol = -0.01,
                                     headgroup = "Any",
                                     ion = "formate",
                                     min_matches = -1,
                                     LIMIT = "All",
                                     peaklist = mypeaks),
               "'min_matches' should be at least 2!")
  expect_error(msms_search_lipidmaps(lipidclass = "phospholipids",
                                     intensity_threshold = 10,
                                     prec_tol = 0.01,
                                     prod_tol = 0.01,
                                     headgroup = "Any",
                                     ion = "formate",
                                     min_matches = "1",
                                     LIMIT = "All",
                                     peaklist = mypeaks),
               "'min_matches' needs to be a number!")
})

# # test the output
#### for now: it returns 0 rows! I don't know why!
# context("msms-search-lipidmaps: output check")
# 
# test_that("Is output correct:", {
#   expect_equal(class(msms_search_lipidmaps(lipidclass = "phospholipids",
#                                            intensity_threshold = 10,
#                                            prec_tol = 0.01,
#                                            prod_tol = 0.01,
#                                            headgroup = "Any",
#                                            ion = "formate",
#                                            min_matches = 2,
#                                            LIMIT = "All",
#                                            peaklist = mypeaks)),
#                "data.frame")
# })