tests/testthat/test-getData.R

In jwist/fusion: Fusion: Objects class definitions for metabolic profiling

# test_that("parse targeted MS works ... Tr", {
#
#   tryptophan <- tMsTestsets[[1]]
#   new <- getData(tryptophan, type = c("sample"), replicates = "last")
#
#   tryptophan[which(getID(tryptophan) == "COV00251"),1]
#   new[which(getID(new) == "COV00251"),1]
#   tryptophan[which(getID(tryptophan) == "COV00344"),1]
#   new[which(getID(new) == "COV00344"),1]
#
#   fi <- getType(tryptophan) == "sample"
#   for (i in 1:32){
#     print(identical(tryptophan[fi,i], new[,i]))
#   }
#
#
#   expect_equal(unname(da[1,1]), 1.026494, tolerance = 1e-6)
#   expect_equal(unname(da[114,1]), 63.60825, tolerance = 1e-6)
#   expect_equal(unname(da[33,15]), 3.140806, tolerance = 1e-6) #serotonin
#   expect_equal(da@obsDescr[[15]]$RT[33], 2.04)
#   expect_equal(unname(da[114,32]), 0.153, tolerance = 1e-6) #IL beta-nicotinamide mononucleotide D3
#   expect_equal(da@obsDescr[[32]]$RT[114], 0.47)
#   expect_equal(getID(da), getID(tryptophan))
#   expect_equal(getType(da), getType(tryptophan))
#   expect_equal(da@.Data, tryptophan@.Data)
#   expect_equal(da@obsDescr, tryptophan@obsDescr)
#   expect_equal(da@varName, tryptophan@varName)
#   expect_equal(da@type, tryptophan@type)
#   expect_equal(da@method, tryptophan@method)
# })
#
# test_that("parse targeted MS works ... AA", {
#   aminoAcids <- tMsTestsets[[2]]
#   expect_equal(unname(da[1,1]), 3.68)
#   expect_equal(unname(da[1,14]), 6.64)
#   expect_equal(unname(da[121,14]), 6.12)
#   expect_equal(unname(da[1,58]), 277.46)
#   expect_equal(unname(da[79,58]), 164.66)
#   expect_equal(da@obsDescr[[58]]$`Area of PI`[79], "54,758.00")
#   expect_equal(da@obsDescr[[59]]$`Area of PI`[123], "8,762.00")
#   expect_equal(getID(da), getID(aminoAcids))
#   expect_equal(getType(da), getType(aminoAcids))
#   expect_equal(da@.Data, aminoAcids@.Data)
#   expect_equal(da@obsDescr, aminoAcids@obsDescr)
#   expect_equal(da@varName, aminoAcids@varName)
#   expect_equal(da@type, aminoAcids@type)
#   expect_equal(da@method, aminoAcids@method)
# })
#
#