tests/testthat/test_1_post_processing.R

In ProMetIS/ProMetIA: Proteomics and Metabolomics Integrated Analysis

testthat::context("Datasets after post-processing")

post_proc.mset <- phenomis::reading(LATMX2::post_processed_dir.c())

testthat::test_that("values", {
  
  testthat::expect_equal(Biobase::exprs(post_proc.mset[["proteomics_liver"]])["Q8C196_Carbamoyl-phosphate synt.",
                                                                              "W627m"],
                         32.1570347762747, tol = 1e-13)
  
  testthat::expect_equal(Biobase::exprs(post_proc.mset[["proteomics_plasma"]])["P01027_Complement C3",
                                                                               "W617f"],
                         32.4223086299966, tol = 1e-13)
  
})

testthat::test_that("dimensions", {
  
  post_proc_dim.mn <- t(sapply(names(post_proc.mset),
                               function(set.c) dim(post_proc.mset[[set.c]])))
  
  # paste(paste(rownames(post_proc_dim.mn),
  #             apply(post_proc_dim.mn, 1, function(x) paste(x, collapse = "|")),
  #             sep = "|"),
  #       collapse = "', '")
  test_dim.vc <- c("clinics|213|42",
                   "proteomics_liver|2187|42",
                   "proteomics_plasma|446|36")
  # test_dim.vc <- c('liv_met_annot_sac|99|42',
  #                  'liv_met_c18n_theix|519|42',
  #                  'liv_met_c18p_sac|8939|42',
  #                  'liv_met_c18p_theix|2060|42',
  #                  'liv_met_hiln_sac|3630|42',
  #                  'liv_prot_F|2187|22',
  #                  'liv_prot_M|2187|20',
  #                  'liv_prot_stra|2187|42',
  #                  'pheno_phenomin|213|42',
  #                  'plas_met_annot_sac|83|42',
  #                  'plas_met_c18n_theix|1920|42',
  #                  'plas_met_c18p_sac|9149|42',
  #                  'plas_met_c18p_theix|3276|42',
  #                  'plas_met_hiln_sac|3402|42',
  #                  'plas_prot_toul|446|36')
  test_dim.mn <- sapply(test_dim.vc, function(x) unlist(strsplit(x, "|", fixed = TRUE))[c(2, 3)])
  mode(test_dim.mn) <- "integer"
  dimnames(test_dim.mn) <- list(c("Features", "Samples"),
                                sapply(test_dim.vc, function(x) unlist(strsplit(x, "|", fixed = TRUE))[1], USE.NAMES = FALSE))
  test_dim.mn <- t(test_dim.mn)
  testthat::expect_identical(post_proc_dim.mn,
                             test_dim.mn)
  
})