inst/tinytest/test_fractions.R

In Vitek-Lab/MSstatsConvert: Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

# Data for testing fractions ----
## Simplest case:
data_for_fractions = data.table::data.table(
    ProteinName = "A",
    PeptideSequence = rep(rep(c("A", "B", "C", "D"), times = 1:4), each = 2),
    PrecursorCharge = 3,
    PSM = paste(rep(rep(c("A", "B", "C", "D"), times = 1:4), each = 2), 3, sep = "_"),
    Mixture = 1,
    TechRepMixture = 1,
    Run = as.character(rep(1:10, each = 2)),
    Channel = rep(c(1, 2), times = 2),
    Intensity = c(1, 1, 1, 1, 2, 2, 1, NA, 1, NA, 0, 2, 1, NA, 1, NA, 1, NA, -0.1, 1.1),
    Fraction = c(1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 3, 1, 1, 2, 2, 3, 3, 4, 4)
)
# Tests ----
## No fractions - do nothing
expect_identical(
    MSstatsConvert:::.handleFractions(data_for_fractions[1:2, ]),
    data_for_fractions[1:2, ]
)
## We find the right features
data_with_additional_cols = data_for_fractions
data_with_additional_cols$techrun = paste(data_with_additional_cols$Mixture, 
                                          data_with_additional_cols$TechRepMixture, 
                                          sep = "_")
.combine = MSstatsConvert:::.combine
data_with_additional_cols$feature = do.call(".combine", list(data_with_additional_cols$ProteinName,
                                                             data_with_additional_cols$PeptideSequence,
                                                             data_with_additional_cols$PrecursorCharge))
data_with_additional_cols$id = paste(data_with_additional_cols$feature, 
                                     data_with_additional_cols$Run, sep = "_")
expect_equal(
    MSstatsConvert:::.getOverlappingFeatures(data_with_additional_cols),
    c("A_B_3", "A_C_3", "A_D_3")
)
## Non-overlapped feature is not considered
expect_equal(
    MSstatsConvert:::.filterOverlapped(data_with_additional_cols, summary_function = mean,
                                       MSstatsConvert:::.getOverlappingFeatures(data_with_additional_cols)),
    data_with_additional_cols[-(c(3:4, 19:20)), ]
)
## Overlap check
### Fails, when overlapped
expect_error(
    MSstatsConvert:::.checkOverlappedFeatures(
        data.table::data.table(
            feature = "A",
            Fraction = c(1, 2, 3),
            Intensity = c(NA, 1, 2)
        )
    )
)
### OK, when not overlapped
fractions_ok = data.table::data.table(
    feature = "A",
    Fraction = c(1, 2, 2),
    Intensity = c(NA, 1, 2)
)
expect_identical(
    MSstatsConvert:::.checkOverlappedFeatures(fractions_ok),
    fractions_ok
)
## 
fractionated = data.table::data.table(
    feature = rep(c("A", "B"), each = 6),
    Fraction = rep(rep(c(1, 2), each = 3), times = 2),
    Run = 1:12,
    Intensity = c(NA, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2)
)
picked_A = MSstatsConvert:::.getCorrectFraction(fractionated[feature == "A"])
picked_B = MSstatsConvert:::.getCorrectFraction(fractionated[feature == "B"])
### More observations win
expect_equal(picked_A, 2)
### Higher average intensity wins
expect_equal(picked_B, 2)
### For full data
expect_identical(
    MSstatsConvert:::.removeOverlappingFeatures(data.table::copy(fractionated)),
    fractionated[Fraction == 2]
)
fractionated_tmt = fractionated = data.table::data.table(
    feature = rep(c("A", "B"), each = 6),
    Fraction = rep(rep(c(1, 2), each = 3), times = 2),
    Run = rep(rep(c(1, 2), each = 3), times = 2),
    Intensity = c(NA, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2),
    Channel = rep(1:3, times = 4),
    Mixture = rep(c(1, 2), each = 6),
    TechRepMixture = 1
)
tmt_unoverlapped = MSstatsConvert:::.handleFractionsTMT(data.table::copy(fractionated_tmt))
expect_identical(
    tmt_unoverlapped[, .(Mixture, TechRepMixture, Channel, feature, Intensity)],
    fractionated_tmt[Fraction == 2, .(Mixture, TechRepMixture, Channel, feature, Intensity)]
)