tests/testthat/test_lfq_with_fractions.R

In MassDynamics/lfq_processing: Processes Proteomics Files for Quantification.

library(LFQProcessing, quietly = TRUE)
library(testthat, quietly = TRUE)
library(here)


acceptance_test<- function(tolerance = 10**-3){
  
  test_that("LFQ with fractions works", {
    
    # remove it if it exists
    if (file.exists("../data/PXD020248/output/proteinGroups_quant.txt")) {
      #Delete file if it exists
      file.remove("../data/PXD020248/output/proteinGroups_quant.txt")
    }
    
    output_folder = "../data/PXD020248/output"
    protein_quant_runner(upload_folder = "../data/PXD020248", 
                         output_folder = output_folder, 
                         protein_only = TRUE)
    
    current = read.table("../data/PXD020248/output/proteinGroups_quant.txt", sep = "\t", header = TRUE)
    expected = read.table("../data/PXD020248/output/expected_proteinGroups_quant.txt", sep = "\t", header = TRUE)
    approx_same = all.equal(expected, current, tolerance = tolerance)
    expect_true(approx_same) #tolerate small differences
  })
  
  test_that("All QCs in LFQ Fractions are created", {
  
  protein_only_split_qc <- c("PCA_proteins", "PCA_screeplot_proteins", "PCA_DE_proteins", 
                               "CV_proteins",
                               "samples_correlations_proteins",
                               "samples_correlations_DE_proteins", 
                               "samples_correlations_scatter_proteins",
                               "missing_by_proteins",
                               "missing_by_samples_proteins",
                               "identifications_proteins")  
  
  output_folder = "../data/PXD020248/output"
  expected_qcs <- file.path(output_folder, 
                            c(paste0("QC_",protein_only_split_qc, ".html"), "QC_Report.html", "QC_Report.pdf"))
  qc_exists <- sapply(expected_qcs, function(x) file.exists(x))
  expect_true(all(qc_exists))
  })
}


acceptance_test()