tests/testthat/test_get_peak_data.R

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

context("test: get_peak_data")

test_that("Testing get peak data 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_peak_data input checks---------------------------------------------

  # Scan Metadata must be of the scan_metadata class
  expect_error(
    get_peak_data(data.frame(test = 1)),
    "ScanMetadata must be a scan_metadata object generated by get_scan_metadata."
  )

  # Scan Number must be an integer
  expect_error(
    get_peak_data(BU_ScanMetadata, "2"),
    "Scan Number must be an integer."
  )

  # Scan Number must be in the range of options
  expect_error(
    get_peak_data(BU_ScanMetadata, 2),
    "Scan Number must be within the range of 29126 & 34291"
  )

  # Min Abundance must be a numeric
  expect_error(
    get_peak_data(BU_ScanMetadata, 30000, "2"),
    "MinAbundance needs to be a numeric value."
  )

  # Min Abundance should be in the range of 1-100
  expect_error(
    get_peak_data(BU_ScanMetadata, 30000, -2),
    "MinAbundance needs to range between 0 and 100."
  )
  expect_error(
    get_peak_data(BU_ScanMetadata, 30000, 101),
    "MinAbundance needs to range between 0 and 100."
  )

  # Create a peak_data object---------------------------------------------------

  # Get peak data for an XML file
  BU_Peak <- get_peak_data(BU_ScanMetadata, 30000, 10)
  expect_true(inherits(BU_Peak, "peak_data"))

  # Get peak data for a raw file
  RAW_Peak <- get_peak_data(RAW_ScanMetadata, 3, 0)
  expect_true(inherits(RAW_Peak, "peak_data"))

})