inst/tinytest/test_dataProcess.R

In MeenaChoi/MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

# Test dataProcess with default parameters ------------------------------------
QuantDataDefault = dataProcess(SRMRawData, use_log_file = FALSE)
QuantDataDefaultLinear = dataProcess(DDARawData, use_log_file = FALSE, 
                                     summaryMethod = "linear")

# Test dataProcess with numberOfCores parameter ----------------------
QuantDataParallel = dataProcess(SRMRawData, use_log_file = FALSE,
                                               numberOfCores = 2)
QuantDataParallelLinear = dataProcess(DDARawData, use_log_file = FALSE, 
                                     summaryMethod = "linear", numberOfCores = 2)

expect_equal(nrow(QuantDataDefault$FeatureLevelData),
             nrow(QuantDataParallel$FeatureLevelData))

expect_equal(nrow(QuantDataDefaultLinear$FeatureLevelData),
             nrow(QuantDataParallelLinear$FeatureLevelData))


# Test dataProcess with technical replicates & fractions ------------------
msstats_input_fractions_techreps = data.table::fread(
    system.file("tinytest/processed_data/input_techreps_fractions.csv",
                package = "MSstats")
)
QuantDataTechRepsFractions = dataProcess(msstats_input_fractions_techreps, 
                                         use_log_file = FALSE)
expect_true(!is.null(QuantDataTechRepsFractions))
expect_true(nrow(QuantDataTechRepsFractions$FeatureLevelData) > 0)