tests/testthat/test_utils_gnps.R

In michaelwitting/genedataRutils: Collection of utility functions to work with .gda files in R

# test_that("Util functions for working with MS2", {
#   
#   # load MS1 data
#   gda_file <- system.file("extdata/20191108_Pesticides_test_Cluster.gda",
#                           package = "genedataRutils")
#   
#   gda_result <- readGda(gda_file)
#   
#   # load MS2 data
#   mgf_files <- dir(system.file("extdata",
#                                package = "genedataRutils"),
#                    pattern = "mgf$",
#                    full.names = TRUE)
#   
#   spectra <- Spectra(mgf_files, source = MsBackendMgf())
#   
#   # add MS1 id
#   spectra_new <- ms2AddId(gda_result, spectra)
#   
#   gnps <- createGnpsFiles(gda_result, spectra_new)
#   
#   gnps_feature <- gnps[[1]]
#   gnps_spectra <- gnps[[2]]
#   
#   # perform tests
#   expect_equal(length(spectra), 512)
#   expect_equal(length(spectra_new), 512)
#   expect_equal(length(gnps_spectra), 320)
#   expect_equal(unique(spectra_new$CLUSTER_ID), c("Cluster_0615", "Cluster_0331", NA, "Cluster_0444", "Cluster_0311"))
#   expect_equal(unique(gnps_spectra$CLUSTER_ID), c("Cluster_0615", "Cluster_0331", "Cluster_0444", "Cluster_0311"))
#   expect_equal(unique(gnps_spectra$scanIndex), c(615, 331, 444, 311))
#   
# })