tests/testthat/test_fragments.R

In rformassspectrometry/PSM: Handling and Managing Peptide Spectrum Matches

test_that("calculateFragments", {
    pqr <- data.frame(
        mz = c(70.065, 198.124,   # a
               98.060, 226.119,   # b
               115.087, 243.145,  # c
               201.098, 329.157,  # x
               175.119, 303.178,  # y
               158.092, 286.151,  # z
               157.108, 285.167,  # y_
               286.151),          # y*
        ion = c(paste0(rep(c("a", "b", "c", "x", "y", "z"), each=2),
                       rep(1:2, times = 6)),
                paste0("y", 1:2, "_"), "y2*"),
        type = c(rep(c("a", "b", "c", "x", "y", "z", "y_"), each=2),
                 "y*"),
        pos = c(rep(1:2, 7), 2),
        z = 1,
        seq = c(rep(c("P", "PQ"), 3),
                rep(c("R", "QR"), 4),
                "QR"),
        stringsAsFactors=FALSE)

    ace <- data.frame(
        mz = c(22.528, 102.544,  # a
               36.526, 116.541,  # b
               45.039, 125.054,  # c
               87.523, 167.539,  # x
               74.534, 154.549,  # y
               66.021, 146.036), # z
        ion = paste0(rep(c("a", "b", "c", "x", "y", "z"), each=2),
                     rep(1:2, times = 6)),
        type = rep(c("a", "b", "c", "x", "y", "z"), each=2),
        pos = rep(1:2, 6),
        z = 2,
        seq = c(rep(c("A", "AC"), 3),
                rep(c("E", "CE"), 3)),
        stringsAsFactors=FALSE)

    expect_message(calculateFragments("PQR", verbose = TRUE),
                   "Modifications used: C=57.02146")
    expect_message(calculateFragments("PQR", modifications = NULL,
                                      verbose = TRUE),
                   "Modifications used: None")

    expect_equal(pqr[1:12,],
                 calculateFragments("PQR",
                                    type = c("a", "b", "c", "x", "y", "z"),
                                    neutralLoss = NULL, verbose = FALSE),
                 tolerance=1e-5)
    expect_equal(pqr[1:4,],
                 calculateFragments("PQR", type = c("a", "b"),
                                    neutralLoss = NULL, verbose = FALSE),
                 tolerance=1e-5)
    ## rownames always differ
    expect_equal(pqr[c(7:8, 11:12),],
                 calculateFragments("PQR", type = c("x", "z"),
                                    neutralLoss = NULL, verbose = FALSE),
                 check.attributes = FALSE, tolerance = 1e-5)

    ## neutral loss
    ## rownames always differ
    expect_equal(pqr[c(3:4, 9:10, 13:15),],
                 calculateFragments("PQR", verbose = FALSE),
                 check.attributes = FALSE, tolerance = 1e-5)

    ## neutral loss (water=cterm disabled),
    ## rownames always differ
    expect_equal(pqr[c(3:4, 9:10, 15),],
                 calculateFragments("PQR",
                                    neutralLoss = defaultNeutralLoss(disableWaterLoss = "Cterm"),
                                    verbose = FALSE),
                 check.attributes = FALSE, tolerance = 1e-5)

    ## neutral loss (ammonia=Q disabled),
    ## rownames always differ
    expect_equal(pqr[c(3:4, 9:10, 13:14),],
                 calculateFragments("PQR",
                                    neutralLoss = defaultNeutralLoss(disableAmmoniaLoss = "Q"),
                                    verbose = FALSE),
                 check.attributes = FALSE, tolerance = 1e-5)

    ## neutral loss + nterm mod, rownames always differ
    tpqr <- pqr[c(3:4, 9:10, 13:15),]
    tpqr$mz[1:2] <- tpqr$mz[1:2] + 229
    expect_equal(tpqr,
                 calculateFragments("PQR", modifications = c(C = 57.02146, Nterm = 229),
                                    verbose = FALSE),
                 check.attributes = FALSE, tolerance = 1e-5)

    ## neutral loss + nterm + cterm mod, rownames always differ
    tpqr$mz[3:7] <- tpqr$mz[3:7] - 100
    expect_equal(tpqr,
                 calculateFragments("PQR", modifications = c(C = 57.02146,
                                                           Nterm = 229,
                                                           Cterm = -100),
                                    verbose = FALSE),
                 check.attributes = FALSE, tolerance = 1e-5)

    expect_equal(ace,
                 calculateFragments("ACE", type = c("a", "b", "c", "x", "y", "z"),
                                    z = 2, neutralLoss = NULL, verbose = FALSE),
                 tolerance = 1e-5)
    expect_equal(ace[1:6,],
                 calculateFragments("ACE", type = letters[1:3], z = 2, verbose = FALSE),
                 tolerance = 1e-5)

    expect_error(calculateFragments("A"), "two or more residues")

    ## issue #200 (mz are not calculated correctly for terminal modifications
    ## and z > 1)
    p <- getAtomicMass()["p"]
    expect_equal(calculateFragments("AA", z = 2,
                                    modifications = c(Nterm = 10),
                                    type = "b")$mz - p,
                                    (calculateFragments("AA", z = 1,
                                                        modifications = c(Nterm = 10),
                                                        type = "b")$mz - p )/ 2)
    expect_equal(calculateFragments("AA", z = 2, neutralLoss = NULL,
                                    modifications = c(Cterm = 10),
                                    type = "y")$mz - p,
                                    (calculateFragments("AA", z = 1, neutralLoss = NULL,
                                                        modifications = c(Cterm = 10),
                                                        type = "y")$mz - p) / 2)

    ## See issue 573 in MSnbase (charge is ignored in neutral loss
    ## calculation)
    expect_equal(
        subset(calculateFragments("PEPTIDEE", z = 3, type = "b"), pos == 7L),
        data.frame(
            mz = c(261.4570693, 255.4535476),
            ion = c("b7", "b7_"),
            type = c("b", "b_"),
            pos = 7L,
            z = 3,
            seq = "PEPTIDE"
        ),
        check.attributes = FALSE # row.names differ
    )

})

test_that("defaultNeutralLoss", {
    expect_equal(defaultNeutralLoss(),
                 list(water = c("Cterm", "D", "E", "S", "T"),
                      ammonia = c("K", "N", "Q", "R")))
    expect_equal(defaultNeutralLoss(disableWaterLoss = c("T", "E", "S", "D")),
                 list(water = c("Cterm"), ammonia = c("K", "N", "Q", "R")))
    expect_equal(defaultNeutralLoss(disableWaterLoss = c("T", "E", "S", "D"),
                                    disableAmmoniaLoss = c("K", "Q")),
                 list(water = c("Cterm"), ammonia = c("N", "R")))
    expect_equal(defaultNeutralLoss(disableWaterLoss = c("Cterm",
                                                       "T", "E", "S", "D"),
                                    disableAmmoniaLoss = c("K", "N", "Q", "R")),
                 list(water = character(), ammonia = character()))
})