tests/testthat/test-normTIC.R

In wesleyburr/subMaldi: Organization and Processing of MALDI-MS Datasets

# -----------------------------------------------------------------------
# Last Updated: March 3, 2021
# Author: Kristen Yeh, Sophie Castel
# Title: testthat: normSpectra()
# -----------------------------------------------------------------------

context("TIC Normalization")
library(subMALDI)

# ----
# TIC
# ----

test_that("One input spectrum yields error", {
  expect_error(normSpectra(dat = Master2, mass_dat = "full_mz", method = "TIC", spectra_cols = c("Before1")))
})

test_that("Correct TIC chosen for norm", {
  med_tic <- normSpectra(dat = Master2, mass_dat = "full_mz", method = "TIC",
    spectra_cols = c("Before1", "Before2", "After1")
  )

  i1 <- sum(Master2$Before1)
  i2 <- sum(Master2$Before2)
  i3 <- sum(Master2$After1)
  i <- c(i1, i2, i3)
  max <- max(i)

  o1 <- med_tic$Before1
  o2 <- med_tic$Before2
  o3 <- med_tic$After1

  expect_equal(sum(o1), max)
  expect_equal(sum(o2), max)
  expect_equal(sum(o3), max)
})

# -------------
# Relative TIC
# -------------

test_that("Difference between raw and norm intensities = TIC", {
  raw8 <- Master2$Before1[8]

  norm <- normSpectra(
    dat = Master2, mass_dat = "full_mz", method = "rel_TIC",
    spectra_cols = c("Before1"))
  norm8 <- norm[8, 2]

  div <- raw8 / norm8
  tic <- sum(Master2$Before1)

  expect_equal(div, tic)
})