tests/testthat/test_get_xic.R

In EMSL-Computing/pspecterlib: PSpecteR Library - Visualization tools for top-down and bottom-up proteomics data

context("test: get_xic")

test_that("Testing get xic function", {

  # Download required test files------------------------------------------------

  source(system.file("tests/testthat/file_check.R", package = "pspecterlib"))
  downfolder <- file_check("downfolder")
  BU_ScanMetadata <- file_check("BU")
  RAW_ScanMetadata <- file_check("RAW")

  # Test get_xic input checks---------------------------------------------------

  # The ScanMetadata object must be of the correct class
  expect_error(
    get_xic(data.frame("Test" = 1)),
    "ScanMetadata must be a scan_metadata object generated by get_scan_metadata."
  )

  # MZ should be a number
  expect_error(
    get_xic(
      ScanMetadata = BU_ScanMetadata,
      MZ = "659"
    ),
    "MZ must be a number."
  )

  # RT should be a range
  expect_error(
    get_xic(
      ScanMetadata = BU_ScanMetadata,
      MZ = 659.8596,
      RTRange = c(60, 58)
    ),
    "RT range must be written as a vector with two numerics, a min and max."
  )

  # Isotope number should include values between 0 and 5
  expect_error(
    get_xic(
      ScanMetadata = BU_ScanMetadata,
      MZ = 659.8596,
      RTRange = c(58, 60),
      IsotopeNumber = c(1:6)
    ),
    "The range of isotope values must be a vector of integers with values between 0 and 5."
  )

  # Charge should include values between 1 and 3
  expect_error(
    get_xic(
      ScanMetadata = BU_ScanMetadata,
      MZ = 659.8596,
      RTRange = c(58, 60),
      Charges = 0:1
    ),
    "The range of charge values must be a vector of integers between 1 and 3."
  )

  # Messages should be TRUE or FALSE
  expect_error(
    get_xic(
      ScanMetadata = BU_ScanMetadata,
      MZ = 659.8596,
      RTRange = c(58, 60),
      Messages = "FALSE"
    ),
    "Messages must be TRUE or FALSE."
  )

  # Create an xic_pspecter object-----------------------------------------------

  # Generate an XIC with an XML file
  BU_XIC <- suppressWarnings({suppressMessages(
    get_xic(
      ScanMetadata = BU_ScanMetadata,
      MZ = 659.8596,
      RTRange = c(58, 60),
      IsotopeNumber = 0,
      Charges = 1
    )
  )})
  expect_true(inherits(BU_XIC, "xic_pspecter"))

  # Generate an XIC with a RAW file
  RAW_XIC <- suppressMessages({
    get_xic(
      ScanMetadata = RAW_ScanMetadata,
      MZ = 1500,
      RTRange = c(0, 1),
      IsotopeNumber = 0,
      Charges = 1:3,
      Messages = NA
    )
  })
  expect_true(inherits(RAW_XIC, "xic_pspecter"))

})