tests/testthat/test_parser_sphingoid_base.R

In michaelwitting/lipidomicsUtils: Utility functions for lipidomics

library(lipidomicsUtils)
context("Test sphingoid base parser")

## tests for correct sphingoid bases -------------------------------------------
test_that("correct sphingoid base is isolated", {

  # sphingolipids, full structure details
  expect_equal(isolate_sphingoid_base("Cer(d18:1(4E)(1OH,3OH)/20:0)"), c("d18:1(4E)(1OH,3OH)"))
  expect_equal(isolate_sphingoid_base("Cer(d18:1(4E)(1OH,3OH)/20:0(2OH))"), c("d18:1(4E)(1OH,3OH)"))
  expect_equal(isolate_sphingoid_base("Cer(d16:1(4E)(1OH,3OH)(15Me)/20:0(2OH))"), c("d16:1(4E)(1OH,3OH)(15Me)"))
  
  # sphingolipids, hydroxyl group level
  expect_equal(isolate_sphingoid_base("Cer(d18:1/20:0)"), c("d18:1"))
  expect_equal(isolate_sphingoid_base("Cer(d17:1/22:0)"), c("d17:1"))

})

## tests for correct sphingoid bases (new sphingoid function) ------------------
test_that("correct sphingoid base is isolated", {
  
  # sphingolipids, full structure details (single lipid)
  expect_equal(isolate_sphingoids("Cer(d18:1(4E)(1OH,3OH)/20:0)"), list(c("d18:1(4E)(1OH,3OH)")))
  expect_equal(isolate_sphingoids("Cer(d18:1(4E)(1OH,3OH)/20:0(2OH))"), list(c("d18:1(4E)(1OH,3OH)")))
  expect_equal(isolate_sphingoids("Cer(d16:1(4E)(1OH,3OH)(15Me)/20:0(2OH))"), list(c("d16:1(4E)(1OH,3OH)(15Me)")))
  
  # sphingolipids, full structure details (multiple lipids)  
  expect_equal(isolate_sphingoids(c("Cer(d18:1(4E)(1OH,3OH)/20:0)",
                                    "Cer(d18:1(4E)(1OH,3OH)/20:0(2OH))",
                                    "Cer(d16:1(4E)(1OH,3OH)(15Me)/20:0(2OH))")), list(c("d18:1(4E)(1OH,3OH)"),
                                                                                      c("d18:1(4E)(1OH,3OH)"),
                                                                                      c("d16:1(4E)(1OH,3OH)(15Me)")))
  
  # sphingolipids, hydroxyl group level (single lipid)
  expect_equal(isolate_sphingoids("Cer(d18:1/20:0)"), list(c("d18:1")))
  expect_equal(isolate_sphingoids("Cer(d17:1/22:0)"), list(c("d17:1")))
  
  # sphingolipids, hydroxyl group level (multiple lipids)
  expect_equal(isolate_sphingoids(c("Cer(d18:1/20:0)",
                                    "Cer(d17:1/22:0)")), list(c("d18:1"),
                                                              c("d17:1")))

})