tests/testthat/test-proteomicsexperiment.R

In marcpaga/pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

context("test-proteomicsexperiment")

test_that("constructor works", {

  assay1 <- matrix(1:9, ncol = 3, nrow = 3)
  assay2 <- matrix(9:1, ncol = 3, nrow = 3)
  assays_list <- list(a1 = assay1, a2 = assay2)
  colData <- data.frame(sample = LETTERS[1:3])
  rowData <- data.frame(peptide = letters[1:3])

  proExp <- SilacProteinExperiment(assays = assays_list,
                              rowData = rowData,
                              colData = colData)

  assay1 <- matrix(1:12, ncol = 3, nrow = 4)
  assay2 <- matrix(12:1, ncol = 3, nrow = 4)
  assays_list <- list(a1 = assay1, a2 = assay2)
  colData <- data.frame(sample = LETTERS[1:3])
  rowData <- data.frame(peptide = letters[1:4])

  pepExp <- SilacPeptideExperiment(assays = assays_list,
                              rowData = rowData,
                              colData = colData)

  expect_silent(PE <- SilacProteomicsExperiment(SilacProteinExperiment = proExp,
                                                SilacPeptideExperiment = pepExp))
  expect_equal(length(metadata(PE)), 7)
  expect_equal(length(metaoptions(PE)), 7)

  expect_is(ProtExp(PE), 'SilacProteinExperiment')
  expect_is(PeptExp(PE), 'SilacPeptideExperiment')

  expect_error(PE <- SilacProteomicsExperiment(SilacProteinExperiment = proExp))
  expect_error(PE <- SilacProteomicsExperiment(SilacPeptideExperiment = pepExp))
  expect_error(PE <- SilacProteomicsExperiment(SilacProteinExperiment = pepExp,
                                               SilacPeptideExperiment = proExp))

})