library(LFQProcessing, quietly = TRUE)
library(testthat, quietly = TRUE)
acceptance_test<- function(tolerance = 10**-3){
test_that("LFQ Experiment where we remove some samples in the experiment design", {
# remove it if it exists
if (file.exists("../data/PXD026936/output/proteinGroups_quant_intensities.txt")) {
#Delete file if it exists
file.remove("../data/PXD026936/output/proteinGroups_quant_intensities.txt")
}
protein_quant_runner("../data/PXD026936", "../data/PXD026936/output", protein_only = TRUE)
current = read.table("../data/PXD026936/output/proteinGroups_quant_intensities.txt", sep = "\t", header = TRUE)
expected = read.table("../data/PXD026936/output/expected_proteinGroups_quant_intensities.txt", sep = "\t", header = TRUE)
approx_same = all.equal(expected, current, tolerance = tolerance)
expect_true(approx_same) #tolerate small differences
expect_false("OE0906_28375" %in% current$file_name) # should be out
expect_true("OE0906_28349" %in% current$file_name) # should be in
})
}
acceptance_test()
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